Flynn, who joined the Terriers on a free transfer from Blackpool in the summer, scored in the 63rd and 78th minute to complete Stan Ternent's side's victory.
In an entertaining first period, Northampton's Karl Hawley struck the crossbar with a close range header before Luke Guttridge's drive was deflected in off Jim Goodwin's knee in the 25th minute.
But the Terriers fought back moments later, with Andy Booth turning home a cross from Liam Dickinson.
Huddersfield's Flynn should have given Ternent's men the lead on the stroke of half time but he dragged a shot off target. However, the midfielder made amends after the interval when he converted Dickinson's pass just after the hour mark.
And Cobblers goalkeeper Chris Dunn gifted Flynn his second goal of the match with 12 minutes remaining when he spilled his 30-yard effort. Northampton substitute, Liam Davis, grabbed a late consolation for the visitors after he nodded home a Ryan Gilligan cross.