McGovern, a 42-year-old grinder who played in the first Boise Open 17 years ago, was at 14-under 128 and leading Brenden Pappas by two shots.
'I'm in a pretty good spot. Everything just feels great right now,' said McGovern, who opened with a 63 on Thursday. 'It is tough to follow up a good round, but I got my mind set before the start of today's round and just kept things easy out there.'
Pappas, also one of the first round co-leaders, shot a 4-under 67 and was alone in second place at 12-under 130.
Another overnight co-leader, Nicholas Thompson, shot a 3-under 68 to share third place with Todd Demsey (66) at 11-under 131. Garth Mulroy (68), Henrik Bjornstad (63) and Matthew Jones (65) were another stroke further back at 132.
McGovern played in the first Boise Open in 1990, the same year he won three times on what was then called the Ben Hogan Tour. He hasn't won anywhere since claiming his only PGA TOUR title at the 1993 Shell Houston Open.
Back to the PGA TOUR is where McGovern hopes he's headed at the end of this year. He was 59th on the money list entering this tournament, about $77,000 out of 25th place -- the last spot to earn PGA TOUR membership for 2008.
'I would love to get back out there and play 30 events next year,' McGovern said. 'That is where you test yourself. That is where you find out how good you really are.'
McGovern remained without a bogey through 36 holes, collecting six more birdies Friday in another spotless round at Hillcrest Country Club.
He tied 2006 champion Kevin Stadler for the low 36-hole score in tournament history. His highlight Friday came with a birdie at the 226-yard, par-3 13th.
'I might be zero for my life hitting that green,' McGovern said. 'But today, I chipped in. So I beat the hole today.'
The cut line fell at 4-under 138, a record-low score for the cut at this event.
Tadd Fujikawa, the 16-year-old Hawaiian making his Nationwide Tour debut, shot a 71 on Friday and missed the cut by three strokes.