McNamara was appointed manager of League Two club York City on 4 November 2015, and his first match in charge came three days later, with a 3–2 away defeat to Accrington Stanley in the FA Cup first round.
In April 2016, York's relegation from the Football League was confirmed by a 3–0 defeat against Accrington.
In October 2016, a 6–1 defeat against the division's bottom club, Guiseley, left York in 20th place in the National League.

Following talks between McNamara and the club, York announced the manager would resign if they failed to gain a "positive result" in their next match, against Braintree Town.
Following a 1–1 draw in that match, McNamara announced he would be stepping down, but had agreed to stay on as manager until a replacement was found.
When Gary Mills was reappointed manager on 16 October 2016, McNamara took on the role of chief executive at the club.
He left this position in March 2018.
McNamara was appointed manager of League Two club York City on 4 November 2015, and his first match in charge came three days later, with a 3–2 away defeat to Accrington Stanley in the FA Cup first round. In April 2016, York's relegation from the Football League was confirmed by a 3–0 defeat against Accrington. In October 2016, a 6–1 defeat against the division's bottom club, Guiseley, left York in 20th place in the National League. 
Following talks between McNamara and the club, York announced the manager would resign if they failed to gain a "positive result" in their next match, against Braintree Town. Following a 1–1 draw in that match, McNamara announced he would be stepping down, but had agreed to stay on as manager until a replacement was found. When Gary Mills was reappointed manager on 16 October 2016, McNamara took on the role of chief executive at the club. He left this position in March 2018.
Jackie McNamara