The Bills had listed Watkins as questionable on their injury report Wednesday. The team noted that Watkins was limited in practice for the first time since complaining of soreness in his surgically repaired left foot following a 13-7 season-opening loss at Baltimore on Sunday.
A team source told ESPN's Dianna Russini earlier on Thursday that Watkins would play as along as he clears pregame tests and can deal with any pain in the foot.
Earlier in the week, Watkins told ESPN that he would be on the field against the Jets.
"I'm doing fine. I'll be fine," Watkins said. "Just was sore after the game. That's expected. Getting prepared for next week."
Watkins will likely be matched up with Jets cornerback Darrelle Revis, who struggled in Week 1 against Cincinnati Bengals wide receiver A.J. Greenin New York's 23-33 loss. Revis said earlier this week he was confident he will bounce back Thursday night against the Bills.
Watkins, the fourth overall pick in 2014, has battled numerous injuries during his career. After missing offseason activities last year because of hip surgery, Watkins missed three regular-season games because of a calf injury and an ankle injury.
He played 42 snaps Sunday against the Ravens, catching four passes for a team-high 43 yards.
Starting left tackle Cordy Glennalready has been ruled out against the Jets. He was hurt against the Ravens, when he aggravated a left ankle injury that forced him to miss three weeks of training camp. Backup Cyrus Kouandjio will start in Glenn's place.
Buffalo is thin at tackle with backup Seantrel Henderson serving a four-game suspension for violating the NFL's substance abuse policy.
The Bills' reshuffled offensive line will be facing a Jets defensive line that sacked Bengals quarterbackAndy Daltonseventimes in Week 1. That line was without star defensive end Sheldon Richardson, who returns for Thursday night's game after serving a one-game suspension.
ESPN staff writer Mike Rodak and The Associated Press contributed to this report.