The defender joins fellow new addition Michael Moore, right, who signed after spending the latter part of last season on loan from Dumbarton.
Henderson spent three seasons at Stair Park before moving to Queen of the South in 2006.
Meanwhile, defender Kevin Nicoll has also agreed a deal for one more season.
Stephen Aitken, Danny Mitchell, Stuart McColm and Steven Noble, who have also already agreed deals with the Third Division side.
The feeling of fans on the team's unofficial website was positive this week.
Onesaid: "Both players may have moved on to bigger clubs over the last couple of years but are returning to a club that they know, made their name and are wanted at.
"The team is taking shape well done to the Management team for bagging their signatures."
Another added: "To sign players that want to play rather than the fact that it is just a pay cheque is a bonus for the club straight away, and we will get many years out of big Murray as I dont imagine he will walk away to another club this time. "