Thumbelina spends time with her mother's farm animals, but is worried that there is no one around of her own size. ("Thumbelina") One night her mother tells her a story about fairies. After being put to bed, Thumbelina imagines that someday she'll be able to find someone to love. ("Soon") As she is humming to herself, Prince Cornelius of the Fairies (Gary Imhoff) flies by her windowsill and is enchanted by her. The two take a ride on Cornelius' Bumble Bee, during which they fall in love. ("Let Me Be Your Wings") During this ride, a toad named Grundel (Joe Lynch) sees Thumbelina and declares to his mother Mrs. Toad (Charo) that he loves her.
Cornelius returns Thumbelina to her windowsill and promises to come back the next day to meet her mother. After he leaves, Thumbelina goes to sleep in her walnut bed, and is kidnapped by Mrs. Toad. When Thumbelina awakes the next morning, she is on a lily-pad far away from home. Mrs. Toad declares that Thumbelina will join their family singing troupe "Singers de Espana". ("On the Road") Thumbelina will also marry Grundel, and the group leaves her alone on the lily-pad to fetch the priest, despite her protests.
Thumbelina's cries for help are heard by Jacquimo, who helps her free of the lily-pad and encourages her to follow her heart and find her way home to her mother. ("Follow Your Heart") Jacquimo himself promises to find Cornelius, who lives in the Vale of the Fairies. Meanwhile, Cornelius has learned of Thumbelina's kidnapping and is out searching for her.
Thumbelina almost reaches home, but she is waylaid by Berkeley Beetle (Gilbert Gottfried) who wants her to join his act at the Beetle Ball. Thumbelina is forced to perform at the Beetle Ball, but at the end is kicked out for being "too ugly". ("Yer Beautiful Baby") Grundel, who is also searching for Thumbelina, tracks down Beetle and forces him to help find Thumbelina.
Searching for the Vale of the Fairies, Jacquimo seeks help from a fleeing rabbit and its pursuerer, a fox. The fox angrily shoves him out of the way and a strong gust of wind blows the swallow into a tree, driving a thorn through his wing. When the cold winter frost arrives, he becomes too weak to fly to the point that he loses consciousness and falls to the ground. The falling snow also causes Cornelius to fall from his Bumble into a pond, where he is frozen in ice. Beetle finds Cornelius and cuts out a block of ice in which the Fairy Prince is trapped to bring to Grundel.
Elsewhere, Thumbelina's mother can only wait at home and hope for the best. ("Soon (reprise)")
With both Cornelius and Jacquimo out of action, Thumbelina takes shelter from the winter frost in a shoe. She is rescued by Miss Fieldmouse (Carol Channing) who tells her that Cornelius is dead. Miss Fieldmouse makes Thumbelina join her to visit Mr. Mole (John Hurt), where Thumbelina is told to sing for him. ("Let Me Be Your Wings (Sun reprise)") They take a walk in Mr. Mole's extensive tunnels, where Thumbelina discovers the unconscious Jacquimo. Mr. Mole tells Miss Fieldmouse that he would like to marry Thumbelina, and she agrees to convince Thumbelina that it would be for the best. ("Marry the Mole") Grundel learns that Thumbelina is to marry Mr. Mole and abandons the frozen Cornelius with Beetle, allowing Thumbelina's little jitterbug friends to light a fire to melt the ice that has trapped Cornelius.
Thumbelina sneaks out of Miss Fieldmouse's home to visit Jacquimo. He wakes, and Thumbelina removes the thorn from his wing. Before she can explain that Cornelius is "dead", Jacquimo flies off, still determined to find the Vale of the Fairies.
The wedding ceremony begins, but when Thumbelina is prompted by the minister, she responds that she cannot marry Mr. Mole. She runs away, and is followed by Grundel, Beetle, and the entire crowd, but Cornelius and the jitterbugs intervene, and Cornelius engages Grundel in a battle which culminates in the both of them falling into a bottomless pit. Thumbelina manages to cause a mountain of jewellery to slide toward her pursuers, frightening them away, and she escapes to the surface, where she is found by Jacquimo, who says that he has found the Vale of the Fairies. They fly there, and after Thumbelina sings ("Let Me Be Your Wings (finale)") the ice thaws and Cornelius, who survived the fall, appears to be reunited with his love. The pair kiss, Cornelius proposes, Thumbelina accepts, and wings sprout from Thumbelina's back. The wedding is celebrated with Thumbelina's mother and Cornelius' family in attendance.
Screenshots during the credits reveal that Beetle resumed his normal, popstar life; Grundel survived the fall with a broken leg and ultimately married a female toad; and Mr. Mole married Miss Fieldmouse.
Character changes include that the Mayfly in the original fairytale has been changed to Berkeley Beetle and Mr. Fieldmouse has been changed to Miss Fieldmouse. Additionally, various characters that Thumbelina only encounters briefly in the fairytale have also been extended, such as the Swallow (in this film, named Jacquimo) who meets Thumbelina relatively early in the film and helps her search for Cornelius in the Vale of the Fairies, as well as the villainous Toad (Grundel) and Beetle who continues to hunt down Thumbelina after she initially escapes from him.
Of note, three of these voice actors (Jodi Benson, Will Ryan, and Kenneth Mars) previously starred in another animated movie adapted from a story by Hans Christian Andersen (Disney's The Little Mermaid, in 1989), in which Jodi was Ariel, Will was the Sea Horse and Kenneth was King Triton. Jodi Benson also played the leading female protagonist in both films.
As of 2008, 25% of critics give it positive reviews at review aggregator Rotten Tomatoes (based on eight reviews) But on the other hand the RT community gave it a score of 55% based on over 100 reviews and it has a "C+" at Box Office Mojo.