The Poland Under-21 international enjoyed a successful loan spell with the Championship club towards the end of the 2009/10 season.
And he has now penned a two-year deal at Pride Park, which will become effective from July 1.
Rams boss Nigel Clough told the club's official website: "We're delighted to have Tomasz signed up for two years.
"His performances towards the end of the season were impressive and we were delighted with what we saw. He instantly struck up a rapport with the supporters who took to Tomasz straight away.
"Tomasz isn't the finished article by any means but he has plenty of talent and potential. We're confident he can develop with us and become a very good player for years to come in a Derby County shirt."
Wigan manager Roberto Martinez admitted he understood Cywka's reason's for moving on.
"There was a deal on the table for him here," Martinez told Wigan's official website. "But Tomasz feels his chances of first team football will be better served at Derby and I respect that decision.
"We wish him all the best in the future."