The final did not take place this year, for only the third time in the competition's history.

Portadown won the cup for the second time, after Cliftonville were disqualified from the competition for fielding an ineligible player in the semi-final replay against Linfield.

[2][3] The following teams were given byes into the first round: 1st Bangor Old Boys, Ballynahinch United, Bangor Amateurs, Civil Service, Dromara Village, Dromore Amateurs, Drummond United, Hanover, Harland & Wolff Sports, Killymoon Rangers, Larne Tech Old Boys, Laurelvale, Magherafelt Sky Blues, Portstewart, Queen's University, Rathfriland Rangers, Seapatrick, Sirocco Works, UUJ and Wellington Recreation.

On 29 April 1999, Cliftonville were disqualified from the competition for fielding an ineligible player in the semi-final replay against Linfield.

The player in question had played for a junior club in an earlier round and was therefore ineligible.