He was appointed to the Cabinet in 1943 as Minister for Lands. Moylan remained in this office until 1948 when the party went into opposition. He served as Minister for Education from 1951 until 1954, when Fianna Fáil lost power again. Moylan lost his Dáil seat at the 1957 general election, but was nominated by the Taoiseach to Seanad Éireann as a Senator later that year. He was later appointed to the Cabinet as Minister for Agriculture, making him the first Senator to be appointed a Government Minister. Seán Moylan died suddenly on 16 November 1957. He was buried in Kiskeam, County Cork. Speaking at an event commemorating the 50th anniversary of his death, Brian Lenihan Jnr suggested that Moylan was "one of the most outstanding military leaders in the War of Independence". Moylan is mentioned in the Irish folk ballad "The Galtee Mountain Boy", along with Dinny Lacey, Dan Breen, and Seán Hogan. The song, written by Patsy Halloran, recalls some of the travels of a "Flying column" from Tipperary as they fought during the Irish War of Independence, and later against the pro-Treaty side during the Irish Civil War.