The Philippines and Djibouti established diplomatic relations on 26 February 1998.

To date, the two countries have signed two agreements – Memorandum of Understanding establishing a Bilateral Consultation Mechanism between the Department of Foreign Affairs of the Philippines and the Ministry of Foreign Affairs and International Cooperation of Djibouti and an MOU between the Foreign Service Institute of the DFA and the Diplomatic Academy of Djibouti.

The Embassy estimates that there are approximately 300 Filipinos working in Djibouti, mainly in the port and in the United States military base. A Philippine Honorary Consulate was established in Djibouti in 2013 to help the Embassy serve the consular needs of the Filipinos.

Philippine exports to Djibouti include machine parts, powdered milk ane cream concentrate, millstones for grinding and steel belted tires.