After the 1975 season, Wirkowski would step down to focus on his role as coordinator of men's interuniversity athletics, stating "I feel we should look for someone that can devote all his time to the program".

Arnott was tasked in rebuilding the program and had struggled early on, going winless from 1990 to 1994, which set a Canadian University football record of 47-straight losses from 1988 to 1995.

Arnott would win the award again in 1997 after leading the Yeomen to a 6–2 record, finishing fourth-place in the OUA, and bringing York to the postseason for the 3rd time in program history.

[30] York began the 2002 season with a victory over the Guelph Gryphons 23–11, followed up by a loss to the Western Mustangs 16–11[31] and a 14–6 win over the Toronto Varsity Blues.

HC Tom Gretes brought in Ottawa Gee-Gees Offensive Coordinator Andy McEvoy to be the team's new OC and was confident that the Lions would have a strong start to the year based on their first 3 opponents.

[41][42] The Lions would finish the year 3–5 with victories over the Toronto Varsity Blues and the Windsor Lancers and qualify for the playoffs despite losing their final regular season game to the undefeated Laurier Golden Hawks, 38–19.

[51] York would go onto lose that game 40–7,[52] but responded with back-to-back wins over the Toronto Varsity Blues (23–20[53] in Overtime) and the Guelph Gryphons (22–15[54]).

[56] York would go onto drop their last 3 games to the Windsor Lancers (41–28[57]), the Queen's Gaels (9–4[58]), and the Waterloo Warriors (13–8[59]); finishing the year with a 1–7 record.

York would lose by wide margins for the rest of the year, except for their 21–20 win over the struggling Toronto Varsity Blues[64] and a surprisingly close loss to the powerful Western Mustangs 11–9;[65] a game which saw both teams tied 8–8 heading into the 4th quarter.

On February 21, 2008, York named former CFLer and Saint Mary's Defensive Coordinator Mike McLean as Head Coach with McEvoy returning as an offensive assistant.

[71] York also didn't manage to set up a full dress roster for the entire 2008 season, with McLean claiming that he had no time to recruit new players after being named head coach and said that the program was in free fall when he arrived.

Mike McLean was also fired on March 16, 2010, with the athletic department citing 'serious philosophical differences' and a 'lack of accountability' as the primary reasons for the removal.

[77] Craney then brought in Montreal Carabins assistant coach Harry LaFlamme and former Western Mustang QB Michael Faulds - who is the record holder for the most passing yards in CIS history - as the new Defensive and Offensive Coordinators respectively.

[87] However, much worse news happened in February, as the team's recruiting coordinator, Daniel Younis, was arrested on charges relating to child pornography and child-luring.

[95] The closest game of the season came against the Waterloo Warriors, where York had a strong 4th quarter that saw RB Connor Anderson score a TD with 14 seconds remaining.

York would recover an onside kick to get one more chance, but kicker Nick Naylor missed a 56-yard FG attempt to win the game as time expired.

[96] The 2015 offseason saw York bring in one of the best recruiting classes in the country, headlined by QB Brett Hunchak, SB Colton Hunchak, WR Jacob Janke, LB Jakob Butler, LB Jakub Jakoubek, WR Nathaniel Pinto, TE Nikola Kalinic, and RB Jesse Amankwaa.

[97][98][99] A lot of the recruiting success can be attributed to Craney also serving as the Head Coach of Team Canada for the IFAF World Junior Championships; a position he held from 2014 to 2016 winning a silver and gold medal over two tournaments.

[106] However, their week 4 loss to Toronto 45–18 was the turning point of the season, as York would lose all their remaining games by a combined score of 220–37 and finish 2–6.

[110] The Lions suffered two blowout losses to start the year to the Western Mustangs and Waterloo Warriors, but put up a strong fight against the #9 ranked Ottawa Gee-Gees; losing 26–17.

On the ensuing field goal attempt, the kick was blocked by freshman LB Matt Dean, leading to a York victory.

Prior to the 2020 season, York hired two-time Hec Crighton trophy winner Tommy Denison as their new offensive coordinator, whom previously was with the Toronto Varsity Blues in 2019.

[128] The following game, despite a very strong defensive effort only giving up 139 total yards of offence, York lost to the Toronto Varsity Blues 25–2; ending a 4-year reign as the Argo Cup Champions.

[129] After that loss, York would drop their final two games by a combined score of 89–9 to the McMaster Marauders and a rematch with Toronto; finishing the year 0–6 and last in the OUA East division.

On April 2, 2022, Warren Craney was put on a leave of absence as the school conducted a thorough review and investigation of the football program with Defensive Coordinator Sammy Okpro being named Interim Head Coach during that time.

During the 2022 season, the Lions finished 1–7 with their lone win coming against the McMaster Marauders, whom had to forfeit the contest for having an ineligible player on their roster.

[133] Olay also was an OUA First-team All-Star returner, with DE Jason Janvier-Messier and LB Matt Dean being named to the Second-team.

Toronto responded with a touchdown from quarterback Kaleb O'Donahue to wide receiver Dane Hurley with 36 seconds remaining, but failed the two-point convert and did not recover the ensuing onside kick.

[144] In week 9, York had a 2–5 record and found itself an opportunity to qualify for the postseason for the first time in 20 years if they were to beat the McMaster Marauders in their final game (with the Laurier Golden Hawks and Ottawa Gee-Gees needing to win their final games to give York an advantage in tie-breakers) to take the 7th playoff seed.

On January 10, 2025, York announced the hiring of Eli Haynes as the new Special Teams Coordinator;[147] replacing Brian Jones from the role.