Hilliman rushed for 89 yards and the two scores while also catching a scoring pass for Boston College (2-3).
Eagles redshirt freshman quarterback Anthony Brown completed 14 of 21 passes for 85 yards and the one touchdown to Hilliman. Freshman back A.J. Dillon rushed for 120 yards and a touchdown.
Junior wideout Jeff Smith was Boston College's leading receiver with 35 yards on two catches.
Central Michigan (2-3) suffered its third straight defeat while totaling a season-low in points.
Chippewas senior quarterback Shane Morris racked up 171 yards on 21-of-42 passing and was intercepted three times. Redshirt freshman Tony Poljan caught three passes for a team-high 61 yards.
The Eagles led 21-8 at halftime after a pair of Hilliman rushing touchdowns in the first and second quarters.
Hilliman scored his first on a 6-yard rush with 10:33 to play in the opening quarter, giving Boston College a 7-2 lead after Hilliman was tackled in the end zone for a safety by Chippewas defensive lineman Deshawn Baker-Williams at 11:46 of the first period.
Dillon scored a 15-yard rushing touchdown at the 4:25 mark of the first to make it 14-2.
Redshirt freshman Kumehnnu Gwilly's 1-yard touchdown rush at 10:24 of the second brought Central Michigan within six after a failed two-point conversion attempt.
Hilliman's second rushing score came with 4:03 left in the first half from 2 yards out. His 23rd career rushing touchdown moved him into a tie for 10th on the Eagles' all-time rushing touchdown list.
Brown connected with Hilliman for a 3-yard scoring pass with 7:40 to go in the third quarter for the game's final score.
Central Michigan is back on the road next Saturday to face fellow Mid-American Conference foe Ohio. Boston College plays host to Atlantic Coast Conference rival and 12th-ranked Virginia Tech on Saturday night.