"There have been times - I think we should be frank - in the last several months where those relations have experienced strains," Mr. Obama said.
Mr. Obama spoke alongside Pakistani Prime Minister Yousuf Raza Gilani amid heightened tensions between their countries following a series of incidents that have marred trust. Tensions reached new heights in November when U.S. forces returned fire they believed came from a Pakistani border post, killing 24 Pakistani troops.
Pakistan broke off ties with the U.S. following that incident and launched a debate about new terms of engagement, including the sensitive issue of CIA drone strikes inside Pakistan's borders.
Mr. Obama said he expects Pakistan's review will result in a "balanced approach that respects Pakistan's sovereignty but also respects our concerns with respect to our national security and our needs to battle terrorists who have targeted us in the past."
The president departed Seoul following his meeting with the Pakistani prime minister and was due back in Washington late Tuesday night.
The Associated Press contributed to this report.