Tiger Woods was just two shots back as he began his bid for what would be his first victory of the year.
The tournament is played over both the North and South courses at Torry Pines with the South Course having been revamped and turned into a 7,500-yard test. Of the 11 players who shot 5-under 67 or better Thursday, all but one played on the North Course.
Those who survive the 36-hole cut will play the final two rounds on the South Course.
Goggin was one shot in front of veteran Jay Williamson and Englishman Luke Donald, who reached the PGA Tour this year through the Qualifying Tournament. None of the top three after Thursday's round has ever won a tour event.
Woods was at 66 along with Chris Riley. Those at 67 included David Frost, Miguel Jimenez, Robin Freeman, David Sutherland, Jerry Smith and Mark O'Meara. Among the leaders, only O'Meara played the South Course Friday. John Daly shot a 3-under 69 on the South.
Goggin, whose best tour finish has been a tie for third at the 2000 Greater Milwaukee Open, finished tied for sixth last week at the Pebble Beach National Pro-Am.