Collins plans to leave the world's largest energy-futures marketplace when his contract expires at the end of the month.
The exchange has not named a successor.
No reason was given for the departure. Nymex and Collins came to a mutual agreement to let the contract expire, the exchange said.
The departure follows months of wrangling with exchange board members, many who resisted Collins's recent push to merge with Boston private-equity firm Parthenon Capital LLC.
Several members of the New York Mercantile Exchange board believed the deal undervalued the Nymex.
Collins has been president of Nymex since July 2001. He previously was a trade representative on the exchange's board while serving as senior vice president of natural-gas trading at El Paso Merchant Energy.
He also was an energy-options maker for Pioneer Futures on the exchange floor and a commercial banker at the Dallas Federal Reserve.