Hughes is the current commander of the Fullerton Police Department's Patrol Division.
The appointment will become effective on Jan. 3. He will replace Kevin Hamilton, who was appointed in August but plans to retire soon.
Hamilton had planned to retire over the summer, but he put it off when Chief Michael Sellers was placed on extended medical leave by his doctor.
Hughes will take over a department that's been plagued with controversy, including the death of a mentally ill homeless man following a confrontation with police.
"Capt. Hamilton has done an outstanding job in assuming the acting police chief position at a very difficult time for the department and the city," said City Manager Joe Felz. "His efforts have been very much appreciated not only by the City Council and myself, but by the community as a whole."
Hughes has been with the department for 28 years.