Flacco will be receiving the playcalls from coach Adam Gase, who decided to retain the duty after consulting with general manager Joe Douglas and members of his offensive staff.
The Jets (0-5) rank 31st in total yards and 32nd in scoring. On Monday, Gase said he was open to a change, but the consensus was the status quo.
"We talked about it as a staff and the guys thought that was the right move to make," said Gase, who has called the plays in each of his 69 games as a head coach. "That was from talking to those guys and seeing if we needed to make any changes in that area and nobody thought that was the reason why it's going the way it's going."
Gase sounded like he is hopeful Darnold can return next week.
Darnold, who sprained the AC joint in the Oct. 1 loss to the Denver Broncos, said Monday in a radio interview that his shoulder was "feeling a lot better" and that he had begun throwing. But he also noted that he was experiencing pain "every now and then."
With the playoffs out of the question, the Jets have opted to take a cautious approach with Darnold, who can return for next week's home game against the Buffalo Bills. That would give him 10 games to rebound from an inconsistent start.
"There's no doubt none of us would say he's anything but tough, but we just want to make sure he's good before we put him out there," Gase said.
"I think he's better than what he was last week," Gase said. "I think the more time you give him, the better he'll feel. I think he's taking the steps that we need him to take to give us an opportunity to take into next week. We'll make that decision when we get there.
"I think he's doing a good job of communicating and letting us know how he feels. ... He's being honest in terms of his pain tolerance, his range of motion, him being able to work on his throwing motion a little bit. He's a quick healer."
Flacco completed 18 of 33 passes for 195 yards and a touchdown, with no turnovers.
"I felt like after the first two series really, I was able to settle in a little bit and actually start to play football and just play, throw the ball well and move when I had to and do all those things," Flacco said.
The Jets are 0-7 when Darnold doesn't start, dating to his rookie year of 2018.