Lisburn Distillery finished bottom of the table and were relegated to Championship 1 after a 2–0 defeat to Ballymena United on 16 April 2013.
[5] 11th-placed Donegal Celtic joined them in Championship 1, after losing on the away goals rule to Warrenpoint Town in the Promotion/relegation play-off following a 2–2 draw on aggregate.
[8][9] Championship 1 runners-up Newry City lost out on promotion, as last season's 11th placed club Lisburn Distillery defeated them 3–2 on aggregate in the Promotion/relegation play-off.
Donegal Celtic played Warrenpoint Town, the runners-up of the 2012–13 IFA Championship 1 in a two-legged tie for a place in next season's NIFL Premiership.
Warrenpoint Town won the tie on the away goals rule to reach the top flight for the first time in the club's history.