The company's CEO Ian King told employees in a note on the BAE Systems' internal website that Brexit would bring a "period of uncertainty", Sky News has reported.
"From early on we have made clear our company view that remaining part of the EU provides greater stability and certainty for the business," he wrote.
"If the UK votes to leave the EU, we would almost certainly enter into a period of uncertainty as the details are worked out."
Over the weekend, BT warned its 81,000 employees that Brexit would hamper the UK economy.
Housebuilder Barratt Developments too told its 6,000 employees in May that Brexit would heighten UK's housing crisis.
Barratt's chief executive, David Thomas, said in a note to staff: "While we are working hard to increase the supply of new homes to help solve the UK’s housing crisis a vote in favour of Brexit would potentially diminish the prospects of sourcing labour from this route - at a time when our industry is struggling with a skills shortage."
Airbus Group, BMW, Citigroup and Siemens are among other employers who have urged their staff to vote remain while Lord Bamford, the chairman of construction equipment manufacturer JCB, has come out in favour of the Leave campaign.