Born in County Roscommon, he was educated in County Leitrem, at University College Dublin and King's Inns. In 1965 Doherty became a member of an Garda Síochána (Irish police force), joining the special branch division in the early 1970's. In 1973 Doherty took a seat on Roscommon County Council, which resulted from the death of his father. In 1977 Doherty was elected to Dáil Éireann as a Fianna Fáil TD. In 1979 Doherty supported Charles Haughey's attempt to take over the leadership of the party.
Haughey was successful and Doherty was rewarded by being appointed Minister for State at the Department of Justice. In the short-lived 1982 Fianna Fáil government Doherty entered the Cabinet as Minister for Justice. In this post he became involved in a series of controversies. After Doherty left office it was revealed in The Irish Times that he ordered the tapping of two journalists home telephones. The newspaper also disclosed that he had been interfering in the workings of the police, known as the Garda Siochana, and the administration of justice for both political and personal reasons. He immediately resigned from the party, however, he re-joined in 1984. In 1989 he failed to be elected as a MEP but instead was elected to Seanad Éireann and became its Cathaoirleach (Chairman).
In January 1992 the phone tapping scandal returned to haunt Fianna Fáil. Doherty announced at a press conference that he had shown transcripts of the conversations to Charles Haughey while he was Taoiseach in 1982. Doherty had always denied this. Haughey denied the claim also, however, he was forced to resign from the government. He then resigned as leader of Fianna Fáil. Doherty re-gained his seat in the subsequent general election and again in the 1997 election.