Burkhart, the NCAA Division II champion, birdied the 11th hole at Merion Golf Club with an 80-foot putt and hit a 30-footer on the 14th to take the lead. Lepp, a junior at Washington, was the Division I champion.
'This course is getting so difficult,' Burkhart said. 'It's hard to get it close. If you're going to make any birdies, you're looking at 20-, 30- or 40-foot putts. Luckily I made a couple of those today.'
Lepp had to rally to win Wednesday's first-round match against Kyle Reifers on the 19th hole, but couldn't overcome Burkhart's consistent play and long putts Thursday.
'I played my worst round of the week,' Lepp said. 'I just struggled early. That was a problem. A couple of missed putts at the end, missed greens where I shouldn't be missing the green -- it just cost me in the end.'
Burkhart, seeded No. 32, was facing 16th-seeded Dillon Dougherty, of Woodland, Calif., in Thursday afternoon's third round. Dougherty, a senior at Northwestern, advanced with a 4 and 2 win over Gary Wolstenholme, a member of Britain and Ireland's 2005 Walker Cup team.
Korey Mahoney, seeded No. 2 and a senior at Eastern Michigan, needed all 18 holes to defeat 31st seeded Brad Tilley 2-up.
Mahoney moved on to face 15th-seeded South African Dawie Van Der Walt.
George Zahringer, 52, also advanced with a win over 16-year-old Oliver Fisher, a teammate of Wolstenholme's. He made a 5-foot putt on the 14th to win 5 and 4.
Zahringer, the 2002 U.S. Mid-Amateur Champion, is seeded 37th and is the oldest player remaining in the field.
'When I'm out there on the golf course, I don't really feel the age difference,' he said.