He was offensive coordinator of the Philadelphia Eagles in 1990, and was promoted to head coach after the firing of his controversial predecessor, Buddy Ryan.
He led the squad to 10- and 11-win seasons in 1991 and 1992 respectively despite the loss of Eagle quarterback Randall Cunningham for the season with a torn anterior cruciate ligament on opening day of 1991. His defense that year, under Bud Carson, led the league in run, pass and total defense. The Eagles were a wild card in the 1992 playoffs, finishing 8–0 at home. In the spring of 1993 the talent that had been drafted by Buddy Ryan began leaving the Eagles en masse; Kotite had poor drafts and the level of talent dropped significantly as a result. In the 1993 season, the Eagles went 8–8; one of the many things for which Kotite was pilloried in Philadelphia was for saying "Hey, eight and eight is great." They began the 1994 season 7–2, with Kotite achieving his seventh win against the Arizona Cardinals, then coached by his former boss, Buddy Ryan. But Kotite, in a fit of braggadocio, told the media that he would keep his options open in the face of rumors that new team owner Jeffrey Lurie was not going to renew his contract. The timing proved disastrous, the Eagles losing all seven of their remaining games, after which Kotite was predictably fired.
After the Eagles let him go, he returned to his home town as head coach of the New York Jets, who had just fired Pete Carroll after one losing season (6–10). Owner Leon Hess named Kotite general manager as well. But under his leadership, the Jets suffered what are still the two worst seasons in franchise history. Kotite won only four games in two seasons, falling to 3–13 in 1995 and 1–15 in 1996 for the worst record in the league both years.  Poorly handled drafts contributed to the rudderless ship, most notably Kotite's first round selection of tight end Kyle Brady over the heavily favored Warren Sapp in 1995. The losing seasons and inept drafts led to mockery; Jets fans started calling him Rich Kotex. Two days before the last game of the 1996 season, Kotite announced he was stepping down as head coach and has never coached in the NFL again in any capacity.
After his coaching days were over, Kotite was involved in two TV promotional commercials, for the USA Network's during the US Open Tennis championships, and for AmeriTrade during the Super Bowl XXXIV pregame show casting him as father of a son who surprises him by telling him he wants to be a Broadway dancer. He continued his media career for the NFL as a regular contributor to NFL Films programming on the NFL Network in particular, including the NFL Top 10 show.