Jeter, 38, had been rehabbing at the Yankees' minor league complex in Tampa but came to the Bronx on Saturday, in part to break up the monotony of the rehab process.
He took batting practice with the team and planned to stay through Sunday.
Jeter hopes that running on his ankle will be the final hurdle before he can start to play in games.
"I feel good," he said. "Everything's moving in the right direction."
Asked if he was encouraged by Jeter's progress, manager Joe Girardi said: "It's a lot better than we were when you look back two weeks ago, four weeks ago. Curious to see him out there running around. It's nice that we get an opportunity to see him, and he's anxious to be back, so this is good."
Jeter was examined late last week by a doctor in Charlotte, N.C., and received clearance to move ahead with baseball activities. The 13-time All-Star hasn't played this season after breaking his ankle in the playoffs last fall and needing surgery.
Jeter sustained another fracture during his rehab in April. Alex Rodriguez faced live pitching on Saturday, taking five simulated at-bats in Tampa. Rodriguez, coming off of hip surgery, walked twice and had a base hit, according to Girardi.
Girardi said he is unsure when Rodriguez will begin participating in simulated games.
"Obviously I think he has to run the bases a little bit more," Girardi said. "And they have not talked to me about the point when he's going to be in a simulated game. I'm not sure when he's scheduled to do that, but obviously if he's taking simulated at-bats, he's gotta be fairly close."
Girardi also said that Francisco Cervelli (broken right hand) is taking some dry swings.
"That's a good sign," Girardi said. "He'll work up to tee and toss shortly."