Carlisle ended their most prosperous period as rapidly as it had started. Back to back relegations in 86 and 87 saw them enter the Fourth division for the first time in 21 years. Their first season in there saw them finish second from bottom but 19 points ahead of relegated Newport County. In contrast, the same year they reached the FA Cup third round but were defeated by eventual champions Liverpool.
The lull in league performance continued. A promotion push in 1990 was thwarted by a last match defeat to Maidstone United and near 20th placed finish in 91 saw manager Clive Middlemass replaced by Aidan McCaffrey. The change in management didn't do much to reverse fortune however and the following season Carlisle finished bottom of the Football League, only avoiding relegation due Aldershot being expelled due to bankruptcy.
Some good then came of a new owner in the form of Michael Knighton whose financial input helped the club steer clear of relegation in 92/93 gain two promotions in 95, 97 to the second division (now 3rd tier) and gain success in the Football League Trophy. Unfortunately the promotions were immediately followed by relegations in 96 and 98 respectively.
In the 1998-99 season Carlisle found themselves in their second successive relegation battle and needing to gain three points from the final game of the season at home to Plymouth Argyle. At 90 minutes the crowd at Scarborough (Carlisle's relegation rival) were already celebrating before the fourth official stated four minutes of extra time would be played at Brunton Park. In the last kick of the game goalkeeper Jimmy Glass, who had signed in an emergency loan deal from Swindon Town after the transfer deadline, scored from a corner kick which he came up to in a last gasp effort to win the match.
In the following years Carlisle continued to narrowly avoid relegation one season after the other. From the 97/98 season through to 03/04 the club only once finished above 22nd in the English fourth tier. The bullet dodging did eventually cease however when in 2004 they lost Football league status for the first time since 1928.