The Yankees captain ran from home to first four times, first to second three times and first to third once on Tuesday at the team's minor league complex.
"Running is probably most important," Jeter said. "Feels good. I'm sure we'll pick it up in the next couple days."
There is no date yet for when Jeter, on the 15-day disabled list for the first time since 2003, will rejoin the lineup. He is six hits shy of 3,000, a chase that's been on hold since he got hurt June 13.
"As soon as I can," he said.
Manager Joe Girardi said Jeter ran at about 50-60 percent, and it will be important to see how he feels Wednesday before deciding when he'll ramp up his sprints.
"The one thing you have to see is you have to see him run at 100 percent and you have to see him recover and maybe do it a couple of days in a row before you can possibly send him out on a rehab," Girardi said before the Yankees hosted Milwaukee.
Jeter could play two minor league rehabilitation games before being activated from the DL, which means he would likely miss the interleague series against the Mets that starts Friday.
"We don't have an exact timetable" for his return, Girardi said.
Jeter also took 24 grounders on the grass, 10 more at his normal infield position and made throws to first base. He took 47 swings during his second day of on-field batting practice.
Also, right-hander Bartolo Colon, sidelined with a strained right hamstring, practiced bunting, a sign that he could pitch against the Mets.
Colon, coming off a 60-pitch, four-inning simulated game on Monday, also threw long toss, ran sprints and did agility drills.
He's on his way back to New York and will be evaluated by the team Wednesday.
"If he's healthy, if we feel that he's ready to go, there's a chance that he's going to pitch," Girardi said.
Converted reliever Mark Prior, on the DL at Triple-A Scranton/Wilkes-Barre because of a strained groin, threw off a bullpen mound for the second time in four days. If there are no problems, he might throw batting practice later this week.