Thompson, 36, was Buddies captain last season but missed much of the campaign due to injury, with St Mirren relegated to the Scottish Championship.
He joined the Paisley club in 2011 following spells at Dundee United, Rangers, Cardiff City and Burnley.
And Thompson, who won 16 Scotland caps between 2002 and 2004, says he is "super motivated" to help St Mirren challenge in the second tier.
"Last season was hugely disappointing missing half the season through injury but with a good pre-season behind me this summer and having worked really hard over the close season I am confident I can be an asset to the team," he told St Mirren's website.
Thompson has made almost 600 senior appearances in club football, scoring 141 goals. He netted three times for Scotland.
St Mirren manager Ian Murray said: "I am delighted to have Thommo on board for the season ahead.
"I know him very well having played together in the past and know he will be a big goal threat for us in the new season, and his experience will be invaluable for the younger players."
Striker Steven Thompson has signed a new one-year contract with St Mirren.