They were in the country ahead of the presidential elections on 8 April.
After interviewing the foreign minister and an opposition candidate, they were detained by plain clothes security officials and questioned for eight hours before being put on a plane.
There has not yet been a response from the Djibouti government.
The reporting team, including BBC’s Africa Security Correspondent Tomi Oladipo, had been granted media accreditation and advised by the government director of communications that they had the necessary authorisation to proceed with their work.
Having been held overnight, without means of communication, they were put on a plane out of the country on Saturday morning without any reason being given.
Press freedom organisation Reporters Without Borders says Djibouti has a poor record when dealing with journalists.
The organisation ranked Djibouti near the bottom of its World Press Freedom Index, at 170 out of 180 countries.
President Ismail Omar Guelleh is running for a fourth term as president on Friday.
He won a disputed election in 2011 with almost 70% of the vote.
The East African nation has a population of only about 800,000 people, but is strategically important.
The country is home to US and French military bases.