In 1994, Hannemann was elected to the Honolulu City Council representing Aiea and Pearl City, and in 1996 he founded the Pacific Century Fellows Program modeled after the White House Fellows Program. He was re-elected to his seat in 1998. He served as Council Chairman from 1998 to 1999. Differences in opinion with then-Mayor Jeremy Harris led to his resignation from the Council in 2000 to run against Harris. Harris won re-election in the September 2000 non-partisan election with enough votes to avoid a run-off that November.