Doherty was born to an Irish family living in Glasgow, Scotland. The family returned home to the Gaeltacht area of Gweedore (Gaoth Dobhair), County Donegal, when he was three years old. He grew up in the Gaeltacht and is a native speaker of the Irish language.
He enrolled in a civil engineering degree course at Dublin Institute of Technology in 1996. He completed two years of the course, earning a national certificate that entitled him to work as a civil engineering technician. He then left third-level education to pursue a job in that field. Doherty later resumed his studies by enrolling in another civil engineering course at Letterkenny Institute of Technology, but dropped out to run for Dáil Éireann in the 2002 general election.
A member of Sinn Féin since 1996, Doherty was a founding member of Sinn Féin Republican Youth and served on its national executive.
In the 2002 general election, Doherty ran unsuccessfully in the Donegal South-West constituency. On 11 June 2004, he ran simultaneously in the local elections for Donegal County Council and in the 2004 European Parliament elections. He failed to win a seat in the European Parliament, but was elected to serve as a county councillor for the Glenties area of Donegal.
Doherty's second attempt to win a Dáil seat, at the 2007 general election, also proved unsuccessful; he received 21.2% of the first-preference vote. However, he was elected to Seanad Éireann by the Agricultural Panel on 24 July 2007.
On 12 July 2010, the High Court granted Doherty a judicial review into why the government had not held a by-election to fill the Dáil seat vacated by Fianna Fáil's Pat the Cope Gallagher when he won election to the European Parliament in June 2009. On 2 November 2010, the High Court ruled that the government had delayed unreasonably in holding the by-election. In response to the ruling, the government announced that the Donegal South-West by-election would be held on 25 November 2010. Doherty stood as the Sinn Féin candidate and won the by-election by a substantial margin, earning 39.8 percent of the first-preference vote. Upon taking his seat in the Dáil, Doherty was appointed Sinn Féin's spokesperson on Finance. However, the Dáil was dissolved on 1 February 2011, at which point Doherty had been a TD for just over nine weeks.
Shortly before the 2011 general election, several newspapers alleged that Doherty had misled the public by stating on various Sinn Féin and Oireachtas webpages that he had formerly worked as a "civil engineer", an occupation that presumes a degree-level qualification. Doherty insisted that he had "always been upfront" about the fact that he had not completed his degree, clarified his educational credentials, and acknowledged that he had qualified as a civil engineering technician and not a civil engineer.
In that election Doherty topped the poll decisively in Donegal South-West, attaining 33.0% of the first-preference vote.
Doherty represented Sinn Féin in the Oireachtas delegation that met the Bundestag's Budgetary and European Affairs committees in Berlin in late January 2012.
It was revealed in June 2012 that Doherty put €8,000 worth of unspent travel and accommodation expenses towards hiring part-time party workers, despite these expenses being supposed to be returned to the Oireachtas under rules introduced in 2010. A report found that he had not breached any expense rules, and cleared him of any wrongdoing.
At the 2016 general election, after a redrawing of constituency boundaries, Doherty was elected to the new five-seater Donegal constituency on the 8th count.
Doherty resides in his hometown of Gweedore and is married to Róisín, a native of County Monaghan and a national school teacher. They have four sons.