After Cincinnati Bengals' quarterback Greg Cook was injured during the 1970 preseason, Carter was traded by the Bills to the Bengals in exchange for a draft choice. He led the NFL in pass completion percentage in 1971 and was third in overall passing. His best game of that season was the opener, in which the Bengals defeated the Philadelphia Eagles 37–14.
Carter completed 22 of 30 attempts for 273 yards, three touchdowns, and no interceptions. In the following year, he split time with Ken Anderson before Anderson took sole possession of the starting job. In 1973, the Bengals decided to go with Anderson as the starting quarterback, but Carter had to miss the entire season due to a broken collarbone.