NCAA Division I Football Championship Subdivision independent schools are four-year institutions in the United States whose football programs are not part of a football conference. This means that FCS independents are not required to schedule each other for competition as conference schools do. As of the 2024 season, Merrimack and Sacred Heart will be competing as independents, as their primary conference, Metro Atlantic Athletic Conference, does not sponsor football. They were previously members of the Northeast Conference which does sponsor the sport. Merrimack and Sacred Heart are confirmed to play as FCS independents in 2024.

Current FCS independents

Former FCS independents

The following is a complete list of teams that have been Division I-AA/FCS Independents since the formation of Division I-AA in 1978. The "Current Conference" column indicates affiliations for the 2023 college football season. The years listed in this table are football seasons; since football is a fall sport, this means that the final season of independent status, or membership in a given conference, is the calendar year before a conference change took effect. Teams in italics are current FBS members; this includes second-year transitional schools that are counted as FBS for scheduling purposes but not bowl game eligibility. Because James Madison met FBS scheduling requirements in its first season in the Sun Belt Conference in 2022 (specifically five home games against FBS opposition), it was allowed to skip the first year of the normal two-year process.