Seattle-bound Flight 68 was approaching takeoff speed when the eagle was ingested into the left engine shortly after 10 a.m. in Sitka, airline spokesman Paul McElroy said.
None of the 134 passengers or five crew members was hurt. The bird collision automatically shut off the plane's engine.
McElroy said the jet braked to a stop about 3,000 feet from the end of the 6,500-foot runway, which ends at the water's edge. The plane then taxied back to the terminal with its single working engine.
The airline was sending a replacement plane from Anchorage to continue the flight later Sunday. Meanwhile, aircraft mechanics were inspecting the sidelined Boeing 737-400 for damage.
McElroy said he didn't know how often such bird strikes occurred.
"It's certainly not unheard of but it is unusual," he said.