"The people of Gibraltar have repeatedly and overwhelmingly expressed their wish to remain under British sovereignty and we will respect their wishes," Johnson said following a meeting with Gibraltar Chief Minister Fabian Picardo.
"I reassured him (Picardo) of both our steadfast commitment to Gibraltar, and our intention to fully involve Gibraltar in discussions on our future relationship with the EU."
The tiny rocky outcrop on Spain's southern tip has long been the subject of an acrimonious sovereignty row between London and Madrid, which wants Gibraltar back after it was ceded to Britain in 1713.
Many of the 33,000 inhabitants of the Rock are now worried that it will be at the mercy of Madrid without the protection of the EU, which has had to intervene in the past to ease rows between the two, particularly over the flashpoint border crossing.
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Gibraltar is also concerned about its flourishing economy, which depends in large part on its access to the EU's single market.
Johnson pledged that the government "will not enter into any process of sovereignty negotiations with which Gibraltar is not content.