PORT-AU-PRINCE, Haiti—Haitian Prime Minister Jack Guy Lafontant resigned Saturday amid calls for him to step down over his handling of a failed plan to raise fuel prices that set off a wave of deadly protests.

Mr. Lafontant told Haiti’s Chamber of Deputies that he sent President Jovenel Moise his resignation letter. Mr. Moise confirmed via Twitter that he had accepted Mr. Lafontant’s resignation along with those of other cabinet members.

The...