Healy was appointed manager of NIFL Premiership side Linfield in October 2015, the club he had supported all his life. He steered the "Blues" to a second-place finish in 2015–16, eight points behind Crusaders. On 7 February 2017, he won his first managerial honour as Linfield beat Crusaders 3–1 in the County Antrim Shield. On 25 February, he was given a six-game general ban after being dismissed from the touchline for the third time of the season. Despite this setback, the "Blues" went on to win the league title in 2016–17, and ended the campaign with a treble after beating Coleraine 3–0 in the final of the Irish Cup. He went on to add the Charity Shield to Linfield's honours with a 3–1 victory over Coleraine at The Oval. They went on to lose to Celtic in the second round of qualification for the UEFA Champions League in the 2017–18 season, and had a disappointing campaign domestically as they finished fourth in the league and exited both cup competitions at the quarter-finals. On 16 February 2018, Healy won his fifth domestic honour with Linfield as they won the Northern Irish League Cup final with a 1–0 over Ballymena United.