The Hyundai driver will take a 1.2s lead over M-Sport’s Ott Tanak heading into Friday’s six asphalt stages in the Czech Republic.
Tanak had assumed an early rally lead after winning Thursday’s opening 2.55km super special held around a racecourse in Prague.
But the Estonian was unable to hold onto the advantage when the rally headed to its second super special stage of the day, Klatovy, 8.92km.
Held in darkness, Neuville completed the two loops of the Klatovy test, 2.2s faster than Tanak to leap from third into the rally lead.
"It was not the greatest stage. I don’t know about the tyres - I think I was in between the wet and the soft, and I decided to go soft at the very last minute," said Neuville.
"The anti-cut devices were reflecting from the lights so you couldn’t see very well, but we had a clean run through."
Tanak felt he struggled to generate sufficient temperature in his soft tyres but still managed to clock a time faster than rest of the Rally1 field.
Championship leader Kalle Rovanpera was third on the stage, 2.9s in arrears, although the effort was enough to see the Finn climb to fourth overall, with eight-time world champion Toyota team-mate Sebastian Ogier ahead in third overall by a tenth of a second.
Ogier admitted he struggled to find "the feeling" in his GR Yaris, dropping 6.1s in the process. The Frenchman posted the fifth-quickest time behind the recovering Hyundai of Esapekka Lappi, who copped a 10s penalty for jumping the start in stage one. The Finn will start Friday in ninth overall.
In sixth on the stage was Hyundai’s Teemu Suninen, ahead of M-Sport’s Pierre-Louis Loubet and Toyota’s Takamoto Katsuta.
Title contender Elfyn Evans was ninth fastest on the stage as he shipped 7.8s following a costly overshoot at right junction.
Evans, who needs to outscore team-mate Rovanpera to prolong the title fight to a deciding round in Japan, will start Saturday 10.7s away from the lead, sitting in eighth overall.
"I had an overshoot at one of the junctions, just locked up at one of the braking zones so it's a shame for that," said Evans.
M-Sport’s Gregoire Munster completed the top 10 on the stage ahead of top WRC2 runner Yohan Russell. In the battle for the WRC2 title, Toksport Skoda’s Gus Greensmith ended stage two third in class and ahead of rival and team-mate Andreas Mikkelsen.
