The Canadian-owned firm is Northern Ireland's biggest manufacturing employer
It employs around 5,000 people in its aerospace business.
The firm's Belfast vice-president Michael Ryan wrote in a letter to staff that the "European debate is very emotional".
The referendum will take place across the UK on Thursday, 23 June.
But, he said that Europe has been good to the company in terms of investment, air travel and giving free movement of goods.
The aerospace firm's Northern Ireland operation exports 95% of its products - 33% of them directly into Europe.
"There are strong views on either side," Mr Ryan wrote.
"But, I can only speak for our company's experience of operating within the EU and explain to you we believe it is better for our company that the UK remains within the EU."
He added that by clarifying the company's position it would "help" employees make "an informed decision on this very important issue".
While Bombardier has stated their support of staying in the EU, other businesses here support the campaign to leave.
William Wright, the founder of bus-maker Wrightbus which employs more than 1,500 people, said he was "totally in favour of getting out".

Researchers from the British Trust for Ornithology used data from a 12-year garden bird survey in their study.
This revealed that many blackcaps from Central Europe had shifted their winter migration, partly because of the supply of garden food in Britain.
The findings are published in the journal Global Change Biology.
"This is the first time that we've shown that feeding birds actually influences the distribution of a bird species across a whole country," lead researcher Dr Kate Plummer told BBC News.
The northern nightingale
Source: RSPB
Until the 1950s, there were hardly any records of blackcaps being in Britain in the winter, but in the past 60 years, researchers say, the number has increased "dramatically".
"We saw that both [climate change and garden feeding] were driving this shift in migration [from the Mediterranean to Britain]," Dr Plummer said.
"Where there was a reliable supply of food, blackcaps were more likely to be seen."
Throughout the 12 year period during which the observations were gathered - by more than 14,000 volunteers submitting a weekly record of the birds in their gardens - blackcaps became more strongly associated with garden food supply.
"So it looks like like they're evolving to adapt to using this big supply of winter food," said Dr Plummer.
Graham Madge, from the RSPB, told BBC News that it was only because "people take such a keen interest" and "monitor birds in these surveys, that we're able to understand the impacts we're having on birds and wildlife".
"It's positive news that blackcap numbers are increasing here, but when it comes to house sparrows and starlings, unfortunately [in these same surveys] we're seeing massive declines," he added.
As for the blackcap's preferred variety of feed - the birds appear to particularly like fats and sunflower hearts.
Follow Victoria on Twitter

Simons blamed construction costs and archaeology requirements for its decision to ask West Dorset District Council to find alternative developers.
West Dorset District Council had agreed funding of up to Â£4m towards the scheme which includes Marks & Spencer and Waitrose stores.
The council said it was "disappointed" by the decision.
The company cited the requirements of English Heritage, including undertaking a full archaeological survey, as making the project financially unviable.
In a letter to the council, Simons' chief executive Tom Robinson said the viability of the second phase of the project had been "marginal for a number of years".
An online petition set up by residents' group Defend our Rich Cultural Heritage backing calls for archaeological investigations of the site, which lies within the walls of the old Roman town, has received almost 4,000 signatures.
Anthony Alford, leader of West Dorset District Council, said: "We remain ambitious for this key town centre site.
"Our vision is to keep Dorchester a thriving shopping destination and keep retailers in our county town."
New council buildings, a library and an adult learning centre have already been built in Charles Street in the first phase of its regeneration.
The boss of Bombardier in Belfast has told its staff that "it is better for our company that the UK remains within the EU".
[NEXT_CONCEPT]
Putting out birdfeed in Britain's gardens is shifting the migration of one particular winter visitor, the blackcap, scientists say.
[NEXT_CONCEPT]
The developer of a new retail area in Dorchester town centre has pulled out of the scheme.