Following his retirement as a player, he enjoyed considerable success as a team manager at Middlesbrough (1973 - 1977), where he secured promotion to Division 1, and Sheffield Wednesday (1977 - 1983), but was less successful at Newcastle United where there was a poor relationship with the fans and Charlton decided to walk away from the job. In 1986 he was a controversial choice as manager of the Republic of Ireland's national team (the first non-Irishman appointed), but he was astonishingly successful at making the most of limited resources (soccer being a minority passion in the republic at the time, the popular code being Gaelic football). Through a policy of employing simple tactics and finding players mainly in the English league who had an Irish-born parent or grandparent but hadn't considered themselves to be Irish, the Republic qualified for the World Cup finals in both 1990 and 1994, famously defeating Italy in 1994.
Following his retirement from management in 1994, Charlton can sometimes be found as a tv football pundit, though he also owns a pub in Dublin, and is Deputy Lord-Lieutenant of Northumbria.