Fischer also had a record nine 3-pointers in 14 attempts and was 8 of 9 from the foul line to surpass the 36 points Hawaii's Dwain Williams had against St. Mary's in 2009. The Cougars are now in the West Coast Conference with St. Mary's after years of battling the Lobos in the Mountain West.
Fischer went scoreless from the field and had four points a day earlier when the Cougars (8-4) lost their tournament opener against Harvard 85-82 in overtime.
Fischer, whose previous high was 30 against Chaminade two seasons ago, had five 3s and 19 points at halftime as the Cougars took a 46-38 lead.
Nick Emery hit 5 of his 10 3-pointers - the Cougars had a tourney record 16 on 28 attempts - and scored 20 points for BYU, which shot 52.5 percent overall.
Tim Williams and Elijah Brown had 16 points each for the Lobos (7-5)