Pepperell, whose hole-in-one the previous day helped him to a share of the first-round lead alongside Tommy Fleetwood and Matt Wallace, shot five birdies as he moved to 8 under overall at Walton Heath.
Eddie Pepperell will take a three-shot lead into the final day of the British Masters as he seeks the second European Tour title of his career - and with it a likely Masters appearance next April.
The world number 50 dropped a shot at the third hole, but led by four strokes when he drained a birdie putt at the fourth.
England's Eddie Pepperell maintained steady progress as made six straight pars before he eagled the 11th hole.
The nearest challengers to Pepperell, who won the Qatar Masters this year and almost made it into Europe's Ryder Cup team, were Matt Wallace (72) and Julien Guerrier, who was 3 under after 15 holes of his second round when play was suspended. Frankly I feel like I'm not hitting the ball that well, really.
Pepperell has finished in the top 10 in five of his last eight events as he targets a second European Tour crown after victory at the Qatar Masters in February.More news: Red Dead Redemption 2 Is 60 Hours Long
'I played terrible in the pro-am on Wednesday, probably the worst I have in a while and wouldn't say I played great today but had that really hot run and it's great to be at the top.' Fleetwood's own round was not without incident, with his only bogey of the day coming after an errant tee shot on the par-three 17th finished in a cup holder in a buggy which had been parked to the left of the green.
"Last week I felt absolutely fine, honestly".
British Open champion Molinari, who leads Fleetwood at the top of the Race to Dubai points list, has been suffering from a back injury since he compiled a ideal 5-0 record in Europe's Ryder Cup triumph last month.
"I'm in a good spot and I'm going to keep pushing", he added. 'I guess people have different thresholds when it comes to mental fatigue and I'm sure I'll feel exhausted eventually, ' Fleetwood said.