It's the latest trouble for the new Dreamliner aircraft after a lithium ion battery problem grounded the fleet in January and a fire erupted on an empty Ethiopian Airlines plane parked at Britain's Heathrow Airport last week.
Flight 007 returned to Boston "as a standard precautionary measure" to check out a maintenance message indicator showing the possible fuel pump problem and landed safely, Japan Airlines spokeswoman Carol Anderson said.
The pilot didn't declare an emergency, and the aircraft burned off fuel before landing, Federal Aviation Administration spokeswoman Arlene Salac said.
The plane left for Tokyo just before 1 p.m. Thursday for a flight of nearly 14 hours. It returned just before 6:30 p.m.
The flight was cancelled, and passengers were being put on other flights.
One of two battery fires that grounded the 787s for three months broke out on a Japan Airlines plane at Logan in January after passengers had exited. The next day, another Japan Airlines 787 leaked 40 gallons of fuel at Logan. The airline said an open valve caused a tank to overflow through a vent.
The 787 is the newest and highest-profile plane from Chicago-based Boeing Co., which has said it stands behind its safety and overall integrity. The 787 is assembled at Boeing plants in Everett, Wash., and North Charleston, S.C.