BA will offer Royal Brunei passengers domestic connections through Heathrow to various UK regional airports and onwards to mainland Europe.
The two airlines started working together in 2014, with Royal Brunei introducing a non-stop Heathrow-Brunei service last year.
Its passengers will be issued all necessary boarding passes upon check-in, with their bags checked through to their final destination.
Karam Chand, Royal Brunei chief executive, said the deal would extend its reach in the "vital" UK and Europe markets.