On February 6, 2016, Floyd signed a one-year, $1 million contract with the Toronto Blue Jays. Floyd entered spring training in competition for the fifth starter role with Aaron Sanchez, Drew Hutchison, and Jesse Chavez. On March 28, it was announced that Sanchez would be the team's fifth starter, and Floyd would begin the season in the bullpen. Floyd left a game against the White Sox on June 25 with a shoulder injury, and was placed on the 15-day disabled list after the game. On June 28, it was determined that he had torn his right lat muscle and would miss 8–12 weeks recovering. Floyd remained on the disabled list for the rest of the 2016 season. He finished the season with a 2–4 record, 4.06 ERA, and 30 strikeouts in 31 innings pitched.