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Duncan won the first race of the round six stage in Frauenfeld in a time of 24min 51.72sec, before coming second in the next race in 25min 1.42sec.
Livia Lancelot, of France, was 4sec ahead of Duncan in the second race.
It was the Palmerston rider’s first race in three months after she injured her wrist when she collided with a photographer during the German round in May.
Duncan (20) could not be reached for comment but her mother, Linda Duncan, said it looked as though Courtney was back to her best.
"She’s probably only been on a bike about five times in three months so it’s pretty incredible what she’s done.
"To perform the way she did when her wrist was probably still a bit sore is just great.‘‘I guess the adrenaline just kicks in and she keeps going."
It was obvious Courtney was thrilled to be back on the winner’s podium in the first race, she said.
"When she came across the finish punching her fist, you could just see she was absolutely stoked."
Duncan burst on to the scene when she secured two wins in her debut showing in the championship in Qatar in March.
She had been a strong contender to win the overall championship but missing the French and Italian rounds through injury set her back in the standings.
It was not the first time Duncan had been set back by injury during her motocross career.
The tenacious rider has had three knee operations and suffered a concussion.
The next race on the circuit is in the Netherlands later this month.