Adam Neely rushed for 218 yards on 30 carries and scored three touchdowns to lead the Eagles to the victory.
Columbia City led 14-0 after the opening period and 28-6 at halftime. The Eagles (1-1) out gained the hosts 355-208 in total yards.
City standout receiver Jared Murphy, who will play at Miami of Ohio, hauled in four passes for 78 yards. His night included a 65-yard touchdown reception.
Whitko quarterback Alex Stoddard scored on an 11-yard run, but was just 4-6 passing for 31 yards with an interception.
Tanner Hughes led the Whitko offense with 13 carries for 85 yards and a nine-yard touchdown run.
Whitko had six turnovers in the loss, including five lost fumbles, to just two turnovers for the Eagles.
Whitko (0-2) hosts Southwood next Friday. Columbia City (1-1) hosts Bellmont.