The story starts with that of an aging king, named William (Dakin Matthews) while he is well-loved, he's very saddened as he has yet had an heir for his kingdom. However, soon he's given a daughter and names her Odette. He holds a big celebration and invites many from different kingdoms, including his friend the widowed Queen Uberta (Sandy Duncan) and her young son Prince Derek. While watching the young prince happily interact with the infant princess, the widowed king and queen think upon the same idea. They decide to have the children meet every summer, with hopes that they would fall in love. However, the evil sorcerer Rothbart can be seen in the back. He cares little for Odette's birth, but he desires King William's throne and kingdom and planned to attack using "the Forbidden Arts." But on the eve of his planned assault, King William's soldiers attacked and destroyed his dark magic. Despite warnings, King William merely banishes the sorcerer. As he's banished, Rothbart vows loudly to William that he will take everything he loves and owns for himself. While many feared King William's mercy, everyone soon forgets the threat and prepare for the age of when Princess Odette and Derek would meet. The story then focuses on the children during their first play date for the summer. While both Uberta and William, as well as Winnie the Pooh (Jim Cummings), Piglet (John Fiedler), Tigger (Paul Winchell), Rabbit (Ken Sansom) and Eeyore (Peter Cullen) and many of the staff make it verbally clear that the marriage is arranged and for that matter they want them to fall in love. The children have quite the opposite feelings for it. During most of their childhood, they have an extreme dislike for one another and most often seen fighting or playing pranks on one another.
It is also seen that once they enter their early teens, Derek and Odette continue to hate each other. An example is Odette's constant winning streak which causes Derek to get jealous and the fact that Odette has a tomato shot at him by Odette. The time forwards to now where both Odette and Derek have now reached adulthood, while both are being pushed into this marriage. It shows that both are getting fed up with the constant pressures of their parents and both insist they dislike the other. However it suddenly changes the moment they both see one another, they instantly fall in love by sight.
Upon watching Odette and Derek dancing, Uberta and William begin a party in victory that they had finally fallen in love. While the festivity is still going on, Odette and Derek are both oblivious as they are still entranced by one another and share their first kiss. The moment after the kiss, Derek immediately announces to arrange the marriage. Everyone begins to celebrate but Odette immediately halts the celebration. While she's flattered by Derek's words, she says she wants to hear what else he has to say beyond her beauty, despite her father's objections to keep quiet. But Derek is speechless and can only answer "What else is there?" Both the parents and Odette are disappointed by his answer, the marriage is called off and William, Odette, Pooh and Piglet leave.
Uberta's left in disappointment that all their years of planning were wasted. During the stormy night, Derek admits to Lord Rogers, his mother's adviser, and his best friend Bromley that he just didn't know what to say to Odette, and he announces he'll prove his love for her. Elsewhere, Rothbart can be seen awaiting for the carriage taking King William, Odette, Pooh and Piglet home. William is left shocked by his daughter's behavior and asks what she wanted Derek to say. Odette answers that she needed to know that he loved her for just being herself. The carriage immediately stops. When William slowly looks out to see why, he sees a figure standing out on the road (not knowing it is Rothbart) and warns Odette,Pooh and Piglet to stay inside. Rothbart wastes no time and uses his magic to turn into a horrible bat-like beast. He kills most of William's soldiers and kidnaps Odette, Pooh and Piglet.
King William's captain is the only one able to make it back to Derek's castle and says they were attacked by a "Great Animal." Upon receiving the news Derek and Tigger rushes to save King William, Odette, Pooh and Piglet. However, he's too late--all that he can find is Odette's locket (which he gave to her as a child) and an injured King William. While Derek tries to ask William who did this, William's left in shock of the events and can only give a warning that "it's not what it seems." Derek is even more confused and asks where is Odette, but William himself can not say anything else other then telling them that "Pooh..Piglet..Odette..is..gone." William dies in Derek's arms (most likely from a heart attack as there were no real visible injuries), and Derek is left shouting out for Odette.
The scene changes to show Rothbart and his assistant "The Hag" (in the credits) feeding a swan at an abandoned castle by the lake (later called Swan lake). It is revealed that the swan is Odette--she has been changed into a swan by Rothbart with Pooh and Piglet. Odette can turn back into a human every night but only when she's on the lake when there's moonlight. Rothbart then tries to persuade Odette to marry him so that he can rule as the king. However she quickly refuses and attempts to run away. Rothbart shows no signs of fear but laughs a bit. As she attempts to leave he informs her that as soon as moon sets she'll turn back into a swan, no matter where she is and Pooh and Piglet decide to stay with her until the others find them. It's shown that in a few days since the events, Derek has been practicing his hunting for several days to find Odette and the "Great Animal," despite everyone says that Odette, Pooh and Piglet are gone.
Elsewhere, Odette has befriended a kind old turtle named Speed and a French-speaking frog named Jean-Bob, who believes he's a prince who was turned into a frog. He wants to kiss Odette to turn back into a prince. Her newest friend is Puffin, a puffin bird who's wing she fixed. While Puffin insists that he wants to repay her kindness, Odette declines since she's under Rothbart's spell. Puffin watches first-hand how Rothbart keeps trying to get Odette to marry him, but to no avail. Rothbart cruelly shows that his powers are growing as he makes the moon set, turning Odette back into a swan. The next day, it's shown that Uberta is hoping to get Derek married so that William's kingdom can have him as a king.
Lord Rogers shows doubt as Derek only wants to marry Odette. However, Umberta reveals to Rogers she's planning a ball for him (though he's oblivious that it's made mainly for him to find a wife). Derek, Rabbit, Tigger and Eeyore have other plans, mostly to take Bromley and go hunt for the "Great Animal" (who he's realized is a shapeshifter), but promises to come home in time for his mother's ball. Meanwhile, Odette and her friends take drastic measures by taking Rothbart's map and make plans to head for Derek's kingdom. As Odette and Puffin make their way to his kingdom, Odette can hear Bromley call for Derek. Despite Puffin's warning, she flies off down into the woods to find Derek. However as Derek sees Odette in her swan form, he believes she's the "Great Animal" and tries to kill her. Puffin manages to save her, and the two fly off trying to avoid Derek's arrows.
They eventually lead him back to the lake and decide that the only way to show him the truth is if she goes to the lake while there's still moonlight. The plan is botched at first because the moon is covered by clouds when Odette lands in the water, but Puffin stops Derek from attacking long enough to buy her time. Derek soon watches in awe and shock that the swan is Odette, the two embrace happily. But their reunion is cut short when Odette hears Rothbart coming. While Derek wants to fight him, Odette insists on him leaving and tells him the way to break the spell is by making a vow of everlasting love. As he leaves, he gives her back her locket and Tigger and Eeyore stay with them but soon Rothbart appears. Out of worry that he'll look for Derek, she announces she'll marry him. Rothbart appears happy but then reveals that he heard her conversation with Derek and tells her she won't see Derek at the ball.
As he leaves, Odette says if he wants to stop her, he'd have to kill her. But Rothbart rebuts her answer by saying that tomorrow has no moon, so she can transform into a human. While Rothbart did get a head's up about Odette's plan, he's still worried about Derek's vow and needs to figure out how to ruin it. He then decides he'll use his magic to make him give his vow to the wrong woman. He then uses his magic to turn the Hag into Odette and sends it as a decoy to the ball. The scene switches to a happy Derek announcing he wants everything set in a swan-like theme and asks where Bromley is. Rabbit announces he wants Bromley to be his best man, upon which the staff and his mother are ecstatic that he's found a new love (though none know it's really Odette).
As they all prepare for the ball, Rothbart takes no chances with Odette. He locks up her in a tower and gives her Bromley for company. As the ball begins, Puffin and Speed plan for Jean-Bob to go down the lake and find an opening to free Odette. But as they set their plan in motion, Uberta and the other attendants get an amazing shock. They see Pooh, Piglet, Tigger, Eeyore and Odette (the Hag in disguise) enter the ball, and Derek obliviously but happily begins to dance with her. Meanwhile, Jean-Bob is fighting for his life with the alligators that are in the lake. Speed and Puffin are able to provide him with some help and distract the alligators so that he can make an opening for Odette to swim out. However, as she breaks out, the alligators then try to eat her, but her friends are able to save her for her to fly to Derek's castle.
Elsewhere, although Derek feels something odd about the Odette he's dancing with, when she presents the swan locket he immediately forgets his worries and decides to make an announcement. As the real Odette finally reaches the castle, she's too late and sees the decoy who stands with Derek. Despite her and the other stuffed animals' many attempts to get Rabbit and Derek's attention to see the truth, she fails and Derek makes the vow to the wrong woman. Believing it is really Odette, Uberta and Rogers celebrate to the news. Rothbart then soon interrupts the celebration and mocks Derek's vow and reveals that not only did Derek make a vow to the decoy, but that because of this error, Odette will soon die.
As Derek, Pooh, Piglet, Tigger, Rabbit and Eeyore turn and try to follow Odette, Odette's life and energy can be seen fading as she flies back to the lake. She soon falls and turns back to her human form. By the time Derek and the stuffed animals reach her, it becomes too late. She dies in his arms as she says she loves him. Angrily Derek announces he made the vow for her, he then sees Rothbart behind him and demands that Rothbert not let Odette die. Rothbart angrily pushes Derek back and answers his demands by saying if only he can defeat him. He then immediately turns into the "Great Animal" and a long battle ensues between them. Derek almost loses this battle, but wins as his friend Bromley (who eventually discovered the opening that Odette used) sends him his arrow and Derek uses it to kill Rothbart.
While Jean-Bob, Speed, and Puffin are glad that Rothbart's gone, they all go quiet as they realize that Odette has not been revived. Derek then tells Odette in his arms, that he loves her for who she is. Upon that declaration of love, Odette immediately awakens. Soon Odette and Derek are married and made king and queen. As Pooh, Piglet, Tigger, Rabbit, Eeyore, Rogers and Bromley watch the couple walk down the streets, Bromley demands Rogers give him an apology because he helped Derek destroy the "Great Animal." However, Rogers plays a trick on Bromely by saying that the "Great Animal" was alive. Upon seeing a somewhat menacing shadow, Bromley believes Rogers and faints from the sight.
However its only Queen Uberta and the shadow was from her unique swan like hairstyle she had for the wedding. Puffin apparently flies off with a group of swans, saying that they were in his army now. As night comes, it is shown that Odette and Derek have had the abandoned castle rebuilt and are residents in it, as party goes on inside. Odette gives Jean-Bob a kiss, but warns him not to be disappointed if nothing happens. Nothing happens though, but Jean-Bob still believes he's a prince when he looks at the reflection in a small pool and sees a handsome man. However its only because another man was standing in his view. As he enters the ballroom, Odette asks Speed if he'd like a kiss too. But Speed declines, saying he's happy as a turtle, they see Jean-Bob approach a woman. The woman screams and faints at seeing Jean-Bob, but he believes its only because "the ladies still fall" for him.
The newlyweds, Odette and Derek, wander around the lake. They stop for a moment to which Odette asks Derek if he'll love her until the day she dies. Derek shakes his head and says no, saying "much longer than that." They kiss as a flock of swans fly over the lake.
- This film was originally supposed to be done after Winnie the Pooh in The Adventures of the Great Mouse Detective, but DisneyAnimeManiac choose to make the film early.
- The storyline continues in Winnie the Pooh Meets The Swan Princess II: Escape from Castle Mountain, Winnie the Pooh Meets The Swan Princess III: The Mystery of the Enchanted Treasure, Pooh's Adventures of The Swan Princess Christmas, Pooh's Adventures of The Swan Princess: A Royal Family Tale and Pooh's Adventures of The Swan Princess: Princess Tomorrow, Pirate Today, which are all made by David Graham (aka BowserMovies1989).
- DisneyAnimeManiac's version was a PAL film with PAL bits from Piglet's Big Movie and Pooh's Grand Adventure: The Search For Christopher Robin and NTSC bits from The Many Adventures of Winnie the Pooh, The Tigger Movie, and Pooh's Heffalump Movie. It is unknown if RatiganRules' remake version will be either an NTSC version or a PAL version.
- John Cleese, who voiced Jean-Bob in the real film, is the current narrator of the Winnie the Pooh franchise.