After starting a clubbaseball team at Brock University in Ontario, Canada and coaching it for the 1995 season, McRae got his first NCAA coaching job as an assistant at Niagara. He coached there from 1996–1997, and Niagara won a MAAC North Division championship in his second season. In 1998, he was an assistant at Winthrop in Rock Hill, South Carolina, before returning to the northeast to become an assistant at Maine from 1999–2001.
Niagara
On July 3, 2001, McRae was named head coach at Niagara, where he attended graduate school. In comments on his reasons for accepting the job, McRae said, "One, my aspirations to become a head coach, and there aren't that many Division I openings that come up each year. Also, it's near home and it gives me a chance to see friends and family again. And my wife is from that area as well." McRae was the head coach at Niagara for three seasons. In his first season, the team finished in 8th place in the MAAC. In both his second and third, Niagara qualified for the MAAC Tournament by finishing the regular season in the top four of the conference. Both teams won 16 conference games, then a program record. In 2003, McRae was named the MAAC Coach of the Year.
Canisius
Following the 2004 season, McRae became the head coach at Canisius. In the three seasons prior to McRae's hiring, Canisius's record was 12–119. In his first two seasons, Canisius finished with a sub-.500 conference winning percentage and did not qualify for the postseason. In 2007, the team finished fourth in the MAAC to qualify for the program's first MAAC Tournament since 1994. It went 0–2 in the tournament. In 2008, Canisius went 41–13 and finished tied for first in the MAAC. The team finished third at the MAAC Tournament, but got the program's first postseason win, 16–7 over Manhattan in an elimination game. McRae won his second MAAC Coach of the Year Award. After finishing second in 2009, the team won the MAAC outright in 2010. The team lost in the MAAC championship game, and McRae won his third MAAC Coach of the Year Award. Canisius qualified for the 2011 and 2012 MAAC Tournaments, and it lost in the championship round again in 2012. It started the tournament with two wins, but lost two extra-inning games to Manhattan in the championship round. In the 2013 season, McRae's team set a program record for wins by going 42–17. McRae won his 300th game as a head coach on March 16, when Canisius defeated Ohio, 16–8. The team finished tied for third in the MAAC to qualify for its seventh consecutive MAAC Tournament. As the third seed in the tournament, Canisius started off 2–0 by defeating second-seeded Marist, 2–1, and first-seeded Rider, 18–7. In the championship round, the team defeated fourth-seeded Siena, 12–11, to advance to the 2013 NCAA Tournament. Canisius was seeded fourth in the Chapel Hill Regional, hosted by #1 national seed North Carolina. The team went 0–2 in the regional, losing 6–3 to North Carolina in the opening game and 14–6 to second-seeded Florida Atlantic in an elimination game. In 2014, Canisius finished the season 40–16 and won the MAAC regular season title. In the MAAC Tournament, the team won its first two games but lost twice to Siena in the championship round. Seven of McRae's players at Canisius have been selected in the Major League Baseball Draft, most recently Garrett Cortright in 2013. Sean Jamieson, taken in the 17th round in 2011, is Canisius's highest overall pick under McRae.
