Toten's mystery-romance story triumphed in the young adult/middle reader award category of the student-chosen literary honour.
Student jurors from grades 7 and 8 dubbed The Unlikely Hero of Room 13 B "a must read."
"[Main character] Adam's caring makes him a hero. The book is full of real emotion. The excellent humour helps to balance the serious issues," the jurors said.
Another juror added: "I loved the twists and turns in the plot. The author created several excellent characters I really cared about and I’d love to read more about them all in a sequel."
The novel, which revolves around a young protagonist struggling with obsessive-compulsive disorder, previously won the Governor General's Literary Award.
Montreal writer-illustrator Anne Villeneuve was the winner in the young children's picture book category for her book Loula is Leaving for Africa.
"Loula has a great imagination," declared the category's student jurors, who are in grades 3 and 4.
"Her trip to Africa was a great way to get away from her stinky brothers. The artwork helps us travel through the story. The drawings are like music and the bright colours are cheerful."
Both authors are first-time winners of the Ruth and Sylvia Schwartz Awards, which were originally established by Sylvia Schwartz in 1976 in memory of her sister, Toronto bookseller Ruth Schwartz.
The prize, now administered by the Ontario Arts Foundation and the Ontario Arts Council, was renamed to honour both siblings.
For the 2014 edition, students from Markham, Ont.'s Aldergrove Public School chose the two winners, who each receive $6,000.