In 1999, Cohen joined head coach Dave Clawson's first-year staff at Fordham and spent three seasons as the defensive coordinator, associate head coach and linebackers coach. Following the 2001 season, Cohen returned to Delaware for four seasons and helped the Blue Hens to the FCS national championship in 2003 with a 40-0 shutout of Colgate in the title game. Delaware went 15-1 that season en route to the national title. He was named the I-AA National Defensive Coordinator of the Year by Football Monthly.
Following his four-year stint at Hofstra, Cohen became the defensive coordinator and linebackers coach at Western Michigan in 2010. In 2011 the Broncos' defense was ranked 10th in the nation in turnovers gained with 31, was sixth in red zone defense and first in the nation in fourth down defense. Three of his players earned All-Mid-American Conference honors with Drew Nowak earning All-America status.
In 2012, Cohen took over the linebacker duties at Rutgers and coached one of the top defensive units in school history. The Scarlet Knights finished fourth in the nation in scoring defense (14.2 points allowed per game), tied for ninth in turnovers gained (32) and 10th in total defense (311.6 yards per game). Linebacker Khaseem Greene earned Big East Defensive Player of the Year honors and was named an All-America after making 136 tackles and forcing six fumbles. Green was a fourth round pick of the Chicago Bears in the NFL Draft.
In 2013, Cohen coordinated a Rutgers defense that ranked third in the nation in run defense.
Cohen is reunited on the Wake Forest staff with defensive coordinator Mike Elko. Elko served as the defensive coordinator at Hofstra from 2006-08 under Cohen.