Anderson seemed set to finish his career with Sunderland, but after 400 appearances and 12 years he signed for Newcastle United for £35,000 in November 1963.
He succeeded Raich Carter as Middlesbrough manager in April 1966 and remained at the club until resigning in April 1973 to be replaced by Jack Charlton. In his time the club were relegated from and promoted to the Football League second division. After leaving Middlesbrough he managed in Greece for AEK Athens FC and in England, where he became boss at Queens Park Rangers, Doncaster Rovers and Bolton Wanderers before giving up management after resigning in 1981. He continued as a scout for various clubs including Newcastle.