Using my own research, I found the last team(s) that was undefeated every season from 1998-99 to present day. Here there are:
1994–95: Connecticut (15–0)
1995–96: UMass (26–0)
1996–97: Oregon (10–0)
1997–98: Utah (18–0)
1998–99: Connecticut (19–0)
1999–00: Syracuse (19–0)
2000–01: Stanford (20–0)
2001–02: Duke‡ (12–0)
2002–03: Duke (12–0)
2003–04: Saint Joseph’s** (27–0)
2004–05: Illinois (29–0)
2005–06†: Florida^, Duke (17–0), Pitt (15–0)
2006–07: Clemson (17–0)
2007–08: Memphis (26–0)
2008–09: Wake Forest (16–0)
2009–10: Kentucky (19–0)
2010–11: Ohio State (24–0)
2011–12: Murray State (23–0)
2012–13: Michigan (16–0)
2013–14: Wichita State* (35–0)
2014–15: Kentucky* (38–0)
2015–16: SMU (18–0)
2016–17: Gonzaga (29–0)
2017–18†: Villanova (13–0), Arizona State^, TCU (12–0)
2018–19†: Michigan (17–0), Virginia^ (16–0)
2019–20: San Diego State (26–0)
2020–21: Gonzaga* (31–0)
2021–22†: Baylor^ (15–0), USC (13–0)
2022–23: New Mexico (14–0)
2023–24: Houston (14–0)
2024–25: Tennessee (14–0)
2025–26: Miami (OH) (24–0 currently)
† all teams lost on the same day, so ^ indicates that the team is chronologically the last that was undefeated
‡ Miami (FL) had the most wins before losing a game (14–0)
* team was undefeated heading into March Madness and lost there
** team was undefeated heading into their conference tournament and lost there