Militants from the extremist group have been persecuting tens of thousands of Christians as they take over large parts of Iraq and Syria.
In some towns and villages Christians were given an ultimatum to pay a tax or face death.
Islamic State (IS) is attempting to set up a Caliphate ruled by strict Islamic law.
The landmark deal between the UK government and officials in Bahrain will bolster security in the Gulf as the treat from the militants continues to rise.
Britain already has four mine hunters permanently based at the Mina Salman Port, but the plans will allow for an increase in the number of warships.
Foreign Secretary Philip Hammond signed the deal and said: "This will guarantee the presence of the Royal Navy in Bahrain well into the future.
"The expansion of Britain's footprint builds upon our 30-year track record of Gulf patrols and is just one example of our growing partnership with Gulf partners to tackle shared strategic and regional threats."
Defence Secretary Michael Fallon said: "This new base is a permanent expansion of the Royal Navy's footprint and will enable Britain to send more and larger ships to reinforce stability in the Gulf. We will now be based again in the Gulf for the long term."