Baker, who allowed five runs on nine hits over six innings in the Twins' 8-6 loss to the Red Sox on Monday, missed 14 games in mid-July after being placed on the disabled list with a right flexor muscle strain on July 7.
He said his elbow "feels average," and that he wants to meet with the club's training staff to see if he can pitch through the discomfort.
"I have no problem pitching with some discomfort as long as it's something that won't get worse," Baker said. "I am OK with it being a little sore. But if you're not effective because of it, it's a different story."
Baker, who had a 3.01 ERA in 17 starts before his injury, has a 4.29 ERA in four outings since being activated from the disabled list on July 23.
"This game is very demanding and you have to be at the top, physically," said Baker, who is 8-6 with a 3.21 ERA on the season. "So it's been tough. It's tough getting the work in in-between [starts]. So we have to talk about it tomorrow and see what they want to do."
Twins manager Ron Gardenhire met with Baker and the training staff after Monday's game, and said the club will do what's best for Baker after meeting again on Tuesday.
"We'll check some things out and see how he feels tomorrow, and then make a decision on what we're going to do," Gardenhire said. "He wasn't feeling great, but he got through it. But it's not a perfect situation, so we're going to talk to everybody and see the best route to go."
Baker said he doesn't want to miss time due to injury, but seemed resigned to going on the disabled list if that's what the doctors think he should do.
"You don't want to be the guy who goes on the DL if that's the decision they make," Baker said. "But you have to do what's best for the team and for yourself, individually."