"P-P-Professor McGonagall! Sh-she said I'd failed everything!"
—Hermione faces her Boggart
Just before she began the 1993-1994 school year, while visiting Diagon Alley with Harry and the Weasley family, Hermione met and adopted a part-Kneazle cat named Crookshanks from the Magical Menagerie. However, her new bond with her cat caused friction with Ron and his pet rat Scabbers, as Crookshanks was always trying to catch the rat. Also at the beginning of this school year, Hermione obtained a Time-Turner from Professor McGonagall so she could double up on classes, though this was kept secret.
When Harry received a Firebolt for Christmas with no note, Hermione reported it to Professor McGonagall, thinking it was sent by Sirius Black, whom everyone believed to be a dangerous murderer who was after Harry. His broom was taken away to be inspected, which caused a temporary rift between the two friends. There was further social strain for Hermione when Ron accused Crookshanks of eating Scabbers, who had disappeared. Hermione poured herself into defending Buckbeak, the hippogriff on trial before the Committee for the Disposal of Dangerous Creatures for attacking Draco Malfoy during a Care of Magical Creatures class. Once the trio reconciled, after Hagrid told Harry and Ron how disappointed he was when they selfishly put the Firebolt and Scabbers over their friendship with Hermione so they apologised, but their attempt failed, as Lucius Malfoy frightened the Committee into deciding that the creature would be executed. Hermione was extremely upset by this news and grew furious to the point of slapping Draco when he mocked Hagrid for being upset about Buckbeak's fate.
That year, Hermione was also among the students who found Remus Lupin to be the best Defence Against the Dark Arts teacher they have ever got. Hermione cleverly deduced that Professor Lupin was a werewolf, based on his Boggart taking the form of a full moon, the timing of his unexplained absences from class, and Professor Snape changing a lesson he took over to the subject of werewolves. However, Hermione did not expose Lupin, presumably because she believed he was a good teacher and did not agree with the prejudice many hold against werewolves. Divination, on the other hand, turned out to be a subject Hermione had no respect for or interest in, and soon dropped the subject after Sybill Trelawney told her that she did not posses the second sight.
Hermione: "Please, sir, the werewolf differs from the true wolf in several small ways. The snout of the werewolf —"
Professor Snape: "That is the second time you have spoken out of turn, Miss Granger. Five more points from Gryffindor for being an insufferable know-it-all."
Ron: "You asked us a question and she knows the answer! Why ask if you don't want to be told?"
— Hermione and Ron in a DADA class
On the day of Buckbeak's execution, the trio ventured down to console Hagrid. While in his cabin, Hermione discovered Scabbers, Ron's lost rat. Hagrid urged them to leave and they witnessed what they thought to be Buckbeak's execution. Before they could return to their dormitory, Scabbers bit Ron and fled. While chasing after the rat, they were attacked by a black dog, which pulled Ron into a tunnel beneath the Whomping Willow. Hermione and Harry hurried after them eventually arriving in the Shrieking Shack, where Sirius Black, whose Animagus form was the black dog, confronted them. They were soon joined by Professor Lupin who was acting strangely, and Hermione told Harry and Ron of her belief that he was a werewolf, which he confirmed. It was revealed that Sirius had been framed for the betrayal of James and Lily Potter, and that the true traitor was Peter Pettigrew, who had been hiding from the world as Ron's pet rat, Scabbers. Hermione also cast Expelliarmus on Snape, knocking him out, at which she was horrified.
Once it had been decided that Pettigrew would be turned over to the authorities, the motley group left the Shrieking Shack. When the full moon appeared, chaos ensued as Lupin transformed, Pettigrew attacked Ron and escaped, and Sirius had to transform in order to protect Harry, Ron, and Hermione from the werewolf. Hermione and Harry rushed to Sirius' aid when they heard him moaning, but then hundreds of Dementors descended on them, come to recapture Sirius. Sirius quickly fainted, and Harry told Hermione to think of something happy and attempt to cast a patronus as he was trying to himself, but they were both unable to cast one. As Harry conjured an uncorporeal Patronus, Hermione passed out leaving Harry to fight the Dementors alone. Harry held them off for a while but was eventually overwhelmed. The Dementors were about to perform the Kiss on Harry, Hermione, and Sirius when a mysterious figure cast a Patronus Charm to repel the Dementors. Harry and Hermione awoke in the hospital wing after being rescued by Severus Snape who conjured stretchers for Hermione, Harry and Sirius. After realising that Sirius's soul was to be destroyed by the Dementor's Kiss and receiving vague though instructive and useful instructions from Dumbledore, Hermione used her Time-Turner to return herself and Harry to a time earlier in the evening. They used this opportunity to rescue Sirius and Buckbeak as it was hinted by Dumbledore that more than one innocent life can be spared. While waiting she discussed their saviour with Harry, and when Harry realised that it was he, she claimed that none but a powerful wizard could have conjured a Patronus to drive away the many Dementors. As evidenced by her assertion that time-travelling is extremely dangerous, Hermione took great personal risk to save Sirius and Buckbeak. At the end of the year Hermione returned her Time-Turner, claiming it caused too much trouble and that she would drop a few subjects instead.