Last year's winner Fitzpatrick recovered from a difficult start at Crans Montana to card a brilliant, best-of-the-day, six under par 64 to move onto seven under for the tournament, two shots behind leader Hideto Tanihara.
The 24-year-old carded two bogeys in the first four holes but followed immediately with three straight birdies on his way to a flawless back nine which left him in a tie for second overnight alongside Denmark's Lucas Bjerregaard.
Willett sits a shot behind on six under par, largely down to a brilliant finish to his round.
Starting on ten, the 30-year-old enjoyed a steady opening nine holes with one birdie before a bogey on one looked to hinder any progress.
He followed with an immediate birdie before birdieing his final three holes to card a 66 for the day.
Scotland's Stephen Gallagher joined Willett in a tie for fourth overnight.