The cost-plus-incentive-fee contract is worth $2.6 billion.
HII said the nuclear-powered carrier arrived at the company's Newport News Shipbuilding facility in Virginia last week for the refueling and complex overhaul. The arrival had been delayed due to "uncertainties surrounding the defense budget and funding of the work."
"Our focus will continue to be on the task at hand: modernizing and improving upon Lincoln's capabilities for another 25 years of successful service," said Chris Miner, NNS vice president, in-service aircraft carrier programs.
"We have worked closely with our Navy partners throughout the budget process and have made good progress getting starting on the planned work during the extended period at Naval Station Norfolk.
"Now that the ship is in dry dock the shipbuilder-Navy team is eager to finish what we've started here at Newport News Shipbuilding."
The refueling and complex overhaul represents 35 percent of all maintenance and modernization in an aircraft carrier's 50-year service life, HII said.
In addition to refueling the ship's nuclear reactors, extensive modernization work to more than 2,300 compartments, 600 tanks and hundreds of systems aboard the carrier will be conducted. Major upgrades to the Lincoln's flight deck, catapults and combat systems will also be performed.