Maloney unsuccessfully contested the 1992 general election as a Labour Party candidate in the Donegal North East constituency, but in the subsequent elections to Seanad Éireann he was elected in the Labour Panel to the 20th Seanad. He stood unsuccessfully in the Donegal North East by-election in April 1996, and he was not elected at the 1997 general election, when his share of the first-preference votes fell from over 11% in 1992 to only 5.5%.
He was defeated in subsequent Seanad elections, but in the local elections in 1999 he was elected a member of both Letterkenny Town Council and of Donegal County Council. Sometime thereafter he left the Labour Party and joined Fine Gael, standing as a Fine Gael candidate for Donegal North East in the 2002 general election, when he won over 10% of the first-preference votes but was not elected. He did not contest any further elections.
Sean grew up in a terraced house in the western Letterkenny estate of Ard O'Donnell on the Lower Ard O'Donnell Road. He married Sally Blake. She gave birth to three boys and made Sean a father. He then moved south of the Swilly to the Oldtown area of the town. As Maloney progressed in the world of politics his living space did too. Sean and his wife bought an old school in the Glencar area of Letterkenny. They redeveloped this building and it's site into a luxurious home. Uncontent with his fall from politics, Sean and his wife moved to Spain.
He is a brother of Eamonn Maloney who served as Mayor of South Dublin from 2006-2007.