MacKinlay was educated variously at St Joseph's School, Wembley; Our Lady Immaculate Primary School, Tolworth; Salesian College (a private Catholic school at the time), now a comprehensive called Salesian School, (Highfield Road, Chertsey), and Kingston College. He worked from 1965 as a committee clerk with Surrey County Council until 1975, when he served as a union official with the National and Local Government Officers Association (NALGO). He joined NALGO in 1965. He joined the Labour Party in 1966. MacKinlay was elected councillor in 1971 in the Royal Borough of Kingston upon Thames and served for seven years.
He stood unsuccessfully for Labour in the following elections:February 1974 General Election: Surbiton
October 1974 General Election: Surbiton
1983 General Election: Croydon Central
1984 European Elections: London South & Surrey East division
1987 General Election: Peterborough
In 2003, MacKinlay famously described Dr David Kelly as "chaff" during Dr. Kelly's appearance before the House of Commons Foreign Affairs Committee. The Committee was investigating issues around the British government's dossier on weapons of mass destruction in Iraq.
Mackinlay's question was:
I reckon you are chaff; you have been thrown up to divert our probing. Have you ever felt like a fall-guy? You have been set up, have you not?
So in this context "chaff" is a reference to the radar countermeasure rather than to something of little value.
It emerged during Kelly's subsequent inquest that Kelly had been deeply upset by his treatment before the Committee and had privately described an MP, assumed to be MacKinlay, as an "utter bastard". MacKinlay reportedly apologised to Kelly's widow for the remark.
According to one report, in May 2007, MacKinlay made the nomination that resulted in Gordon Brown having enough nominations to be certain of not facing a contest over the leadership of the party. However, another report states that the decisive nomination was made by Tony Wright with MacKinlay yet to nominate at that point.
On 24 July 2009, he announced that he would not stand at the next General Election due to disillusionment with the way he felt other MPs had caved in to party pressure rather than standing up for their beliefs. He said that the final straw was the failure of a number of Labour MPs who had expressed support for Gary McKinnon, awaiting extradition to the U.S. on computer hacking charges, to vote for a review of the extradition treaty.
On 1 October 2009, MacKinlay accepted a public apology and libel damages from the BBC over allegations made on BBC2’s Newsnight programme that he proposed an amendment to a British government motion on expenses of MPs so he would benefit financially.
On 4 September 2009, MacKinlay supported the views of Eric Joyce on the Afghanistan war.
Mackinlay argued that initiatives should be taken to encourage Irish participation in the Commonwealth. He brought forward a motion on the issue in the House of Commons. Ireland had participated in the Commonwealth in the 1930s and 40s. Mackinlay's view was that historians were wrong to say that Ireland had left the Commonwealth in 1949. This was, he said, because the Commonwealth, to the extent that it existed, was nothing like the Commonwealth of today. He felt that the London Declaration formula that permitted republics to participate in the Commonwealth had not been offered to Ireland as an option, though he felt it was not too late to do so. He argued that Ireland should be formally invited to join and that the Commonwealth was its "natural place".
He is a keen researcher on World War I history, travelling and discovering Ireland, and is an honorary patron of Tilbury Football Club. He and his wife Ruth (née Segar); have three children. While an MP, he employed his wife as his personal assistant. He is a member of the editorial board of Total Politics, a political magazine, of which his daughter, Sarah, was editor until August 2009.
He was given the Freedom of Gibraltar in 2010.
MacKinlay publicly supports the abolition of the monarchy and is identified as a republican.
On 28 June 2008, it was reported by the Mail Online (Daily Mail) website that Mackinlay had received a warning from the Prime Minister's Office after MI5 discovered that he was holding meetings with a suspected Russian spy, Alexander Polyakov, officially a counsellor at the Russian Embassy in London. It was also claimed that MacKinlay had been targeted by aides of Russia's richest man, Oleg Deripaska, as a 'stooge' for use in a High Court battle.