He earned Conference USA Coach of the Year honors in 1997, after leading the Bearcats to a 7–8–3 record.

In 2001, he was named head men's soccer coach at Dartmouth College, compiling a 106–74–31 record with the Big Green.

He led Dartmouth to five Ivy League championships, and to the NCAA tournament seven times, including two Sweet Sixteen berths.

On January 2, 2018, Cook was named the 12th coach of the Penn State Nittany Lions' men's soccer program.

He led the team to a 6–9–2 record, but posted a six-win improvement in 2019, his second season at the helm, going 12–4–3 and leading Penn State to its first NCAA Tournament berth since 2014.