He attended Lawnswood Comprehensive school in Leeds before going on to the University of Edinburgh, where he graduated with an MA in Economic and Social History. He is a life member of the Edinburgh University Union, part of the Edinburgh University Students Association. In February 2006 he was elected Rector of the University of Edinburgh.
He joined the youth wing of the Labour Party when he was 15 and remained a member until 1991. At this point he became involved in the Scottish Green Party's student movement. He ran as a candidate for this party in the 1995 council elections, the 1999 Scottish Parliamentary election and a 2001 council by-election. He was first elected in the 2003 Holyrood election, as the second Green MSP in the Lothians. He was a member of the Scottish ParliamentFinance Committee and was also substitute member of the Enterprise and Culture Committee. He committed substantial time to promoting social enterprises and co-operatives, as a Green alternative to the current system. He also used the position to call for sustainable procurement guidelines, support ethical investment campaigns, and make the case for Scottish utilities being in public ownership. As the Green speaker on Transport, Mark Ballard supported campaigns against the Dalkeith by-pass and the M74, for the trams in Edinburgh and for a better and cheaper public transport system. As a Lothians MSP he helped raise awareness of community initiatives such as the campaign to resist a huge superstore development in Portobello, supporting the calls for congestion charging in Edinburgh, assisting universities wanting to make the switch to Fairtrade and opposing tuition fees for students. The latter in particular helped him win support amongst Edinburgh's student community.
In February 2006 he stood for election as Rector the University of Edinburgh standing against MP Boris Johnson, pro-Palestine journalist John Pilger and former Scotsman editor Magnus Linklater. The profile of the election had been raised by Johnson's candidature. The election took place on 15 and 16 February 2006, with a record turn out of almost 8000. A system of Single Transferable Vote was used. In the final round Mark Ballard received 3,597 votes against Magnus Linklater's 3,052 and was elected. He was formally installed on 9 June 2006 in a ceremony in the University's Old College. Present at this ceremony were the Chancellor of the University, HRH Prince Philip, Duke of Edinburgh, the University Vice-Chancellor and Principal, Professor Timothy O'Shea, and Mark Ballard's predecessor as Rector, Labour MP Tam Dalyell. In this capacity he worked on issues of concern to students and university staff, including playing a prominent role in the movement which led to the complete abolishing of student tuition fees in Scotland in 2008. He was succeeded as Rector in 2009 by journalist Iain Macwhirter, whose campaign drew on many of Ballard's supporters.