The Australian, who smashed an unbeaten century against the same opposition last season, had managed just 66 runs in four innings this year but came out in determined mood ready to entertain a packed Wantage Road.
He plundered five sixes and 13 fours, and shared an 81-run stand in 8.5 overs with skipper David Willey (20) as the Steelbacks reached their target of 165 with seven balls to spare.
Earlier the Foxes lost 4-48 in their last seven overs with Australian Andrew Tye taking 3-30.
Tye got the key wicket of Louis Kimber (41 off 27) before knocking over Callum Parkinson and taking a fine return catch to dismiss Harry Swindells in the final over.
When Northamptonshire batted, Lynn powered through the gears targeting Parkinson with a pair of fours off the third over.
He smashed Naveen-Ul-Haq through extra cover and cut him slightly squarer for another boundary before dispatching Colin Ackermann and Parkinson for sixes over cow corner to bring up his half-century off 42 deliveries.
The Queenslander was especially severe on Josh Hull, taking 20 from his second over, including a big six over the family stand at deep midwicket and crashing him through extra cover.
Lynn swept Parkinson for six and hit him for four down the ground to go into the 90s before reaching his century and bringing up the Steelbacks win by clubbing Rehan Ahmed for six and two fours off consecutive deliveries.
At Chelmsford, New South Welshman Nathan Ellis bagged 3-10 to help defending champions Hampshire record their highest margin of victory - 118 runs - in the competition after bowling hosts Essex out for 96.
It was the Eagles's first T20 defeat of the year, due largely to a James Vince ton which set up a daunting 215-run target.
Vince is now the competition's highest run scorer and by chalking up his fifth T20 century is now only behind West Australian Michael Klinger in Blast hundreds (eight).
Victorian Glenn Maxwell took 2-19 and struck 29 off 22 balls but couldn't stop Birmingham from maintaining their winning streak in the North Group.
The Bears' run came to an end after a 17-run loss to the Derbyshire Falcons with Wayne Madsen continuing his fine form.
Madsen came into the game on the back of three half-centuries and a hundred and delivered another white-ball masterclass with an unbeaten 71 off 52 balls to lead the Falcons to 5-174.
The Bears' hopes of equalling their best start in the competition with a fifth victory quickly faded as they slipped to 4-45 in the powerplay, with England's Moeen Ali falling for 16.
Maxwell briefly threatened with 29 off 22 balls but the Bears came up short on 9-157.
