Speaking at a news conference in Geneva, Roberto Azevedo said that leaving the "EU will have an important trade component, clearly".
Trade has been a hot topic in the upcoming EU referendum, with Out campaigners claiming the UK could do a free trade deal with the rest of the EU after voting to leave, but Remain campaigners arguing this would not happen.
Those advocating Leave have also said that as an independent country the UK would be free to make its own free trade deals with the rest of the world.
However, Azevedo suggested that the impact will be dependent on the deals made both with the EU and other countries.
"If [Britain does vote to leave the impact] depends on the terms of separation, it depends on the relationship that would ensue between the EU and the UK, it depends on the negotiations that the UK would have with WTO members to clarify what the rights and obligations would be at that point in time," he added, according to Reuters.
Azevedo's comments come as Prime Minister David Cameron warned younger generations that a vote for Brexit would lead to an economic shock.
The Confederation of British Industry as well as IHS Global are among organisations who have recently said there would be an economic shock to the UK on leaving the EU.
CBI director general Carolyn Fairbairn said last month: "The savings from reduced EU budget contributions and regulation are greatly outweighed by the negative impact on trade and investment."
However, Leave campaigners have said that this amounts to fear mongering, as employment and the economy would continue to grow after a Brexit vote.