Boretti's coaching career began at Endicott, a Division III school located in his hometown of Beverly, Massachusetts. After spending the 1995 season at Endicott, he was an assistant at Davidson from 1996 to 1998 and Brown from 1999 to 2000.
Franklin & Marshall
Boretti's first head coaching position came at Division III Franklin & Marshall, where he replaced Mark Cole ahead of the 2001 season. Boretti spent five seasons at the school, where he had an overall record of 116–82. In 2002, Boretti's second season, the Diplomats went 31–10 and shared the Centennial Conference title with Johns Hopkins. The team made the conference tournament, where it lost in the second round. In 2005, Franklin & Marshall won the Centennial outright and defeated Johns Hopkins in the conference championship series to receive an automatic bid to the NCAA Tournament. There, it lost a pair of 1–0 games to Rowan and Messiah.
Columbia
Boretti was hired at Division I Columbia ahead of the 2006 season; he replaced Paul Fernandes, who had been promoted to associate athletic director. After finishing third in the Gehrig Division in 2006 and 2007, the Lions won the division with a 15–5 record in 2008. They defeated Rolfe Division champion Dartmouth in the Ivy Championship Series to advance to the NCAA Tournament, Columbia's first since 1976. At the Conway Regional, the Lions lost to host Coastal Carolina, 10–2, and second-seeded East Carolina, 9–0. The Lions had their first winning season under Boretti in 2010, when they went 27–20 and won the Gehrig Division for the second time. They then lost to Dartmouth in the Ivy Championship. Under Boretti, Columbia's home field, Robertson Field at Satow Stadium, underwent renovations in 2007 and 2010. After finishing third in the division in 2011 and 2012, Columbia won back-to-back Ivy League titles in 2013 and 2014, defeating Dartmouth in the championship series in both years. At the Fullerton Regional in 2013, Columbia went 1–2, getting its first NCAA Tournament win against third-seeded New Mexico. At the Coral Gables Regional in 2014, the Lions received the third seed and went 0–2. From 2006 to 2014, six Columbia players have won major awards in the Ivy League, including Dario Pizzano, who was named Rookie of the Year in 2010 and Player of the year in 2012. Four Lions have been selected in the Major League Baseball Draft, with the highest pick being Pizzano, a 15th-round selection of the Seattle Mariners in 2012.
Head coaching record
Below is a table of Boretti's yearly records as a collegiate head baseball coach.