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Lillis took his first job as coach for Macclesfield Town. Later, he worked for Huddersfield Town before he became assistant manager of Scunthorpe United in 1996. His first job as manager came in 1999, when he took the job at Halifax Town, a job he had until September 2000. In 2002, after John Gregory had employed him as a coach at Derby County, and Gregory was suspended from the job, Lillis was for a short time in March 2003 caretaker manager of Derby.
In March 2003 he also became assistant manager to Sammy McIlroy who was manager of Northern Ireland, and held the part time job until October 2003. After that he became assistant manager to Sammy McIlroy at Stockport County, and when McIlroy quit the job in November 2004, Lillis became caretaker manager of the club until the 18 December 2004 when Chris Turner took over as the new manager.
On 30 May 2006, Lillis once again took over as assistant manager to Sammy McIlroy at Morecambe. Both Lillis and McIlroy left the club by mutual consent on 9 May 2011, after a disappointing twentieth place finish in Football League Two.
In December 2011, he returned to his first club, Huddersfield Town, to become their new Academy Manager. Two months later he was appointed caretaker manager after the sacking of Lee Clark. He remained in this role until the appointment of Simon Grayson as the new manager, but was never needed as Town had no matches in the intermittent period.
Following Grayson's sacking on 24 January 2013, he became caretaker manager again, this time taking charge of 5 match, beginning and ending with Town's FA Cup 4th round tie against Leicester City. His 5 games in charge saw Town draw with Leicester in the cup, get a 1–0 win over Crystal Palace, before losing 3–0 to Lillis' former club, Derby County, then holding the runaway leaders Cardiff City to a goalless draw, then getting a 2–1 win against Leicester in the cup replay at the King Power Stadium, setting up a 5th round tie with Premier League side Wigan Athletic.