Stenson, meanwhile, reeled off six birdies in a row around the turn before putting the finishing touches to his stunning 62 with a birdie to sit in a tie for second place alongside Wu Ashun on nine under, one shot clear of early clubhouse leaders Joakim Lagergren and Jason Scrivener.
The early risers found low scores hard to come by following persistent overnight rain and blustery morning conditions but the weather improved throughout the day and Fitzpatrick, Wu and Stenson were able to take full advantage.
Fitzpatrick made a quiet start to his round, opening up with a bogey before getting the shot back at the fourth to reach the turn in 36.
The Yorkshireman caught fire as he began the back nine, making a birdie at the short tenth before coolly slotting in from 30 feet for another at the 13th.
The 24-year-old made another enormous birdie putt from some 35 feet at the short 15th to take the outright lead on nine under.
And he kept his foot on the gas, sending his approach into the 16th to around three feet and tapping in to open up a two shot lead.
Fitzpatrick knocked in his close range putt at the 18th for a closing birdie to move to 11 under, and with Stenson also making a birdie at the last, Fitzpatrick stayed two strokes clear.
After his round, Fitzpatrick said: "It’s been great the past two days. Everything going to plan.
"This summer has been really big for me in a lot of things. I have struggled the past three or four summers, and not had the results I have wanted or what I was working for, and this year we have been a little bit different.
"I have worked on my back foot shot along with a lot of other good practice stuff we have been doing away from the tournaments, so it is paying off so far."
Stenson, meanwhile, began his second round seven shots behind the early clubhouse leaders and gave himself more work to do after dropping a shot at the first.
But he was soon moving in the right direction, notching birdies at the second and third holes to go under par for the round.
After safely parring the next four holes, the Ryder Cup star kicked off his brilliant burst of scoring by walking in his 15 foot birdie putt at the eighth before holing his ten foot effort for another gain at the ninth.
He began his back nine with a monster birdie putt at the short tenth before sending his approach into the 11th green to four feet and rolling in for a fourth straight gain.
The volume went up a notch when Stenson made it five in a row from eight feet on the 12th green to jump to seven under.
And he lifted his tee shot to six feet at the 13th before knocking in to grab a share of the lead.
Four straight pars from Stenson allowed Fitzpatrick to move two shots clear and the Swede made his ninth birdie of the day from close range at the last to move to nine under.
Starting at the tenth tee, Wu made four birdies in a row from the 11th before closing his front nine with another gain at the 18th.
Back to back bogeys at the second and third threatened to derail his round but he made further birdies at the sixth, seventh and eighth to join Stenson on nine under.
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