He stood unsuccessfully as a SNP candidate for the House of Commons in the Glasgow Anniesland constituency in the 1997 General Election before standing in the Glasgow Maryhill constituency in both the 1999 and 2003 Scottish Parliamentary elections.
Wilson was also elected chair of the SNP's Glasgow Regional Association in 2001.
In the aftermath of the 2003 election performance of the SNP he became convinced that a change of direction was needed by the SNP leadership. After discussing this with various SNP members he was persuaded to contest the leadership himself and launched a challenge against the SNP leader, John Swinney.
His campaign focused on the issue of centralising the control of the party away from the branches and activists, and what he argued was the trend of placing the SNP ideologically in the centre ground of politics, away from the party's traditional position on the left-of-centre.
In the leadership contest that ensued at the SNP's 2003 Conference Swinney received 577 votes from those delegates voting to Wilson's 111.