He has managed the Hershey Wildcats, Montreal Impact, Vancouver Whitecaps, Detroit Ignition, and Rochester Rhinos.

A former midfielder, he played collegiately at George Mason before appearing at the professional level for Orlando Lions and Maryland Bays and indoors with Hershey Impact, Harrisburg Heat, and Pittsburgh Stingers.

[7] Lilley officially became head coach of the USISL A-League expansion franchise Hershey Wildcats on January 20, 1997, immediately following his retirement as a player the weekend prior.

He was able to guide Hershey to one Northern Conference and three Atlantic Division titles as well as the 2001 A-League National Championship final, which they lost 2–0 to the Rochester Raging Rhinos.

In 2006, he led the Whitecaps to their first North American championship since 1979, when they defeated the Raging Rhinos 3–0 at PAETEC Park becoming the first team in USL First Division history to win the title on the road.

As Rochester's 2018 season looked increasingly shaky following years of declining attendance, Lilley departed the club to become the head coach of the Pittsburgh Riverhounds.

[14] Under Lilley's coaching, the Riverhounds underwent drastic improvement when compared to the prior two seasons, in which the club had finished with a losing record.

The Riverhounds held a clean sheet through the first four matches, the first time the club had achieved such a streak since the United Soccer League formed in 2011.

[17] Lilley and the Riverhounds won the USL Championship Player's Shield with the top record in the league at the close of the 2023 regular season, but fell to Detroit City FC in the playoff quarterfinals.