Ted Goin (66) and Dave Eichelberger (68) share third place at 9-under-par, followed by Jim Dent, who is alone in fifth following a 7-under 65 Saturday.
Gilder, who defeated Hale Irwin last week to win the SBC Senior Open, tried to distance himself from the pack on the front nine at Nashawtuc Country Club. He drained a 15-foot birdie putt at the third and two-putted from 35 feet for birdie to reach 8-under-par for the championship.
The 51-year-old knocked a 6-iron to 20 feet to set up birdie at the eighth and made it two in a row with another 20-footer at the ninth. He made the turn at 10-under-par before cruising to seven consecutive pars on the second nine.
Gilder collected another birdie at the par-3 17th when his tee ball landed 18 feet from the hole. He had an opportunity to extend the lead at the par-5 closing hole but three-putted from 40 feet for par.
'I putted very well today,' said Gilder, a three-time winner on the elder circuit. 'I did not hit my irons well at all. It was all the putter. I'm fortunate to still have the lead.'
Thorpe was 3-under for his round when he reached the par-4 14th. He drained a five-foot birdie there and made it two in a row with a two-footer at the next.
Thorpe, who won The Tradition in April, parred No. 16 but managed to hole a 10-footer for birdie at the 17th and close the round with a two-foot birdie at the last after finding a greenside bunker.
'I had nine or 10 one-putt greens today and when that happens, I usually shoot pretty low,' said Thorpe. 'I need to shoot another 65. Hopefully the putts will be falling again.'
Allen Doyle, the 2001 Senior Tour Player of the Year, shares sixth place with Tom Jenkins, Jack Spradlin and Wayne Levi. The group stands at 7-under-par 137.
Two-time defending champion Larry Nelson fell off the pace Saturday with a 1-over 73. He is tied for 18th at 4-under-par, seven shots behind Gilder's lead.
Full-field scores from the FleetBoston Classic