He is quitting the company to set up his own agency and return to writing ads.
In March this year, Pe was also appointed as the chief creative officer of DDB's sister agency WWAV Rapp Collins, with responsibility for both agencies.
During his time at the network, he was widely regarded as having improved DDB's creative output in the region.
The agency's group president and chief executive, Gil Chus, said the agency would miss his "touch and creative skill".
DDB Philippines has clients including McDonald's, Johnson & Johnson, the credit card company Bankard and the national newspaper Malaya.