He was educated at Castlebay Secondary School on the island of Barra and the Nicolson Institute in Stornoway on the Isle of Lewis before attending Strathclyde University where he played shinty[3] and in 1992 gained a degree in civil engineering.

After qualifying as a teacher at Jordanhill College in 1996, he then taught the first Gaelic Medium Class at Salen and Acharacle Primary Schools in Argyll on the Scottish mainland.

At the 2001 general election, MacNeil stood as the SNP candidate in Inverness East, Nairn and Lochaber, coming second with 25.6% of the vote behind the incumbent Labour MP David Stewart.

In April 2006, he and former MP Martin Bell wrote to the Prime Minister Tony Blair calling for all appointments to the House of Lords to be suspended in the wake of the scandal.

[7] In November 2006 he won the Best Scot at Westminster section of the Scottish Politician of the Year awards for instigating the inquiry into possible abuse of the honours system.

[16] In July 2019 MacNeil criticised the then Conservative leadership candidate, Boris Johnson for stating that learning English is essential for immigrants.

[24] The SNP selection process for all MP candidates, including in seats the party holds, was scheduled to take place before the October conference MacNeil had chosen as a time he would consider re-joining the group.

In 2007, the Sunday Mail reported MacNeil had "kissed and fondled" two girls aged 17 and 18 in an Orkney hotel room while his wife was in hospital pregnant with their third child.