The 17-year-old Fujikawa, trying to be the youngest champion in the 50-year history of the tournament, was at 14-under 202.
Fujikawa has struggled since turning pro last summer, missing the cut in nine straight events. He made history last year at the Sony Open when he was 16 as the youngest player in 50 years to make the cut on the PGA Tour.
David Ishii, the 1990 Hawaiian Open champion and 14-time Japan Golf Tour winner, shot a 73 and was 7 under. The 52-year-old Ishii is seeking his fourth Mid-Pac title.
John Lynch (71), the 2005 winner, was third at 5 under heading into the final round, two strokes ahead of Darren Summers (74).
The winner Sunday will earn $13,500 from the $64,000 purse.