Ivica Olic looks to be on his way back to Hamburg, with Andre Schurrle increasingly likely to join Wolfsburg.
The 46-year-old, who took charge at the Stadion De Goffert in July 2011, was under contract until the end of this season but will now stay in Nijmegen for a further 12 months.
"NEC are developing in many areas," Pastoor said.
"The ambitions of the club, the atmosphere in Nijmegen and the further professionalisation of the club - I can help contribute to all of that."
NEC are seventh in the Eredivisie standings and in contention for a Europa League play-off place.