McHugh was criticised by Eileen Doherty, a sister of Donegal County Councillor and Provisional IRA member Eddie Fullerton, who was assassinated by loyalists in 1991. Doherty claimed McHugh and other Fine Gael councillors in Donegal had snubbed a number of commemorative events and opposed the building of a monument in Fullerton's memory in Buncrana. Fullerton was the third elected official in the Republic of Ireland to be assassinated. In Manchester in October 2011, McHugh became the first Fine Gael TD to address delegates from the British Conservative Party. He described it as an "opportunity." On 15 July 2014, he was appointed as Minister of State at the Department of Communications, Energy and Natural Resources and at the Department of Arts, Heritage and the Gaeltacht with responsibility for Gaeltacht Affairs and Natural Resources. His appointment was met with criticism as his knowledge of the Irish language was at a basic level, although he subsequently received praise for his efforts to improve his language skills to the point where he could conduct lengthy interviews in the language. RTÉ Radio 1 produced the radio documentary Fine Gaeilgeoir, narrated and produced by Máire Treasa Ní Cheallaigh, following McHugh's efforts to improve his Irish over the course of a year. Shane Ross later wrote of his fear of having what he described as a "Joe McHugh moment", meaning being a non-Irish speaker to a Gaeltacht ministry. In February 2016, McHugh was heavily criticised for allocating 93% of Gaeltacht grants to the Donegal Gaeltacht, which is located in and beside his constituency. This revelation led to calls for McHugh to appear before the Dáil Public Accounts Committee to explain such a disproportionate allocation of funding. McHugh subsequently denied the claims. At the 2016 general election, McHugh was elected to the new five-seater Donegal constituency on the 11th count. The following May, he met Charles, Prince of Wales, and Camilla, Duchess of Cornwall, during their day visit to the county. He was appointed as Minister for Education and Skills on 16 October 2018. He was not re-appointed to the Government of the 33rd Dáil in June 2020, and declined the offer of appointment as a Minister of State. In September 2020, McHugh became Chair of the Committee on European Union Affairs. In May 2022, McHugh announced that he would not stand at the next general election. On 6 July 2022, McHugh resigned the Fine Gael party whip