Less than five months after taking Hartlepool United up via the Vanarama National League Promotion final, he has returned to the competition after an agreement was reached.
Challinor, 46, enjoyed a promising start to life in League Two with Hartlepool sitting in tenth place - with only goal difference keeping them from a play-off place.
But County made the Pools boss their number one target to replace Simon Rusk, who was sacked last week with the club sitting outside the top seven.
He says the ambition at Edgeley Park was just too much of a lure and agreed to take over despite a strong relationship with fans and players at Pools.
Stockport confirmed their capture after days of speculation.
In a club statement, Challinor explained: “The chance to return to County and help make club history was too good an opportunity to miss.
“The excitement surrounding the club and the investment that has been put into it, on and off the pitch, makes County an incredibly attractive proposition for any manager. This can be seen by the influx of new talent the club has recruited over the last month, with the likes of Robert Elstone and Bolton Wanderer’s Antoni Sarcevic joining.
“Now is the time to capitalise on this and take the fans on the journey they deserve, making Stockport County a force to be reckoned with and getting back to the Football League. I look forward to being re-united with County fans on Sunday.”
Challinor is no stranger to taking a step back to try and move forward.
In 2011, then in charge of National League North newcomers Colwyn Bay, he left for AFC Fylde - at the time in the Northern Premier League Division One North.
He was 90 minutes away from securing the Coasters a place in the EFL but now wants to make it two promotions to League Two inside 12 months.