AP1st Team All-Pro (1964, 1969) NEA1st Team All-Pro (1966) UPI1st Team All-Pro (1967)
AP 2nd Team All-Pro (1965, 1966, 1967, 1968)
NEA 2nd Team All-Pro (1967, 1969) The Sporting News2nd Team All-Pro (1969)
Baughan was selected in the second round of the 1960 NFL Draft by the Eagles as the 20th player chosen overall and became an immediate starter for the team at right side linebacker. Baughan played the next 10 years in the NFL and was voted all-pro four times. At the conclusion of his rookie season, the Eagles won the 1960 NFL Championship, which remains the last league title for the franchise. Baughan was selected to the Pro Bowl for the first of nine times that year, finishing with three interceptions. All told, Baughan would make the Pro Bowl five out of six years during his time with the Eagles. During a December 12, 1965 in a game against the Pittsburgh Steelers, the Eagles intercepted a team-record nine passes en route to a 47-13 win over the Steelers. Six of those points came courtesy of Baughan when he returned a first quarter interception by Steelers quarterback Bill Nelsen thirty-three yards for the lone touchdown of his NFL career.
By 1966, the number of games the Eagles won had sharply declined and Baughan decided that he wanted out of Philadelphia. However, George Allen, who was entering his first season as an NFL head coach with the Los Angeles Rams, won the right to Baughan's services by sending two players (linebacker Fred Brown and defensive tackle Frank Molden ) to the Eagles in return. Baughan and Allen would develop a strong relationship, spending extensive time studying game film together. Baughan would later state that he learned more about football from Allen than anyone else.
Baughan was chosen to be the Rams defensive captain and was in charge of signal calling for the unit. He was selected for the Pro Bowl in each of his first four seasons with the Rams and was also named 1st Team All-Pro three times. After an injury-plagued 1970 season, in which he played in only 10 games, Baughan retired from the NFL. From 1972–1973, he was an assistant coach and defensive coordinator at Georgia Tech. In 1974, Allen, now the head coach of the Washington Redskins, talked Baughan into a brief return to the NFL as a player-coach for the Redskins. At the conclusion of that season, Baughan retired. He finished with 18 interceptions (including 1 returned for a touchdown) and 10 fumble recoveries in 147 games played.