​​The diplomatic relations between Indonesia and Djibouti has been established since 1979. Indonesia and Djibouti do not have the country’s representatives in each country. The Indonesian Embassy to Ethiopia is concurrently accredited to the Republic of Djibouti, while the embassy of Djibouti to Japan is concurrently accredited to Indonesia.

The two countries  have signed a bilateral Agreement on Economic and Technical Cooperation, on 2 May, 1997 by both Minister of Foreign Affairs. In addition, Chairman of Chamber of Commerce of the two countries has signed an MoU of cooperation on October 2015. The MoU is intended to enhance cooperation between the two organizations and to promote and facilitate business related activities.  

Based on data from the IMF Directory of Trade Statistics accessed on 1 May, 2016, imported goods from Indonesia until the year 2015 ranks third after China and Saudi Arabia. The total trade value between Indonesian and Djibouti for the year 2016 reaches USD 211.444,3 million (calculation by Central Statistic Agency of Indonesia). The total value of trade is decreased when compared to 2015 which amounted to USD 278.268,4 million. The decline occurred due to the decline in the value of Indonesia's exports to Ethiopia, taking into account that all of Ethiopian import goods must be processed through Djibouti's port. 

The products of Indonesia which have been on the Djiboutian market among others: food products, beverages, transportations, chemicals and petroleum products. The Indonesian Sarong product has a high demand in DJibouti because of its high quality.

To assist the Indonesian Embassy in Addis Ababa, in November 2013, the Government of Indonesia appointed a Honorary Consul of the Republic of Indonesia in Djibouti. The Honorary Consul acts on behalf of the Indonesian government in Djibouti in order to enhance Government to Government relations, people to people contact, and business to business contact.

According to data from Directory of Trade Statistics of IMF accessed on 1 May 2016, until 2015, imported goods from Indonesia ranks third after PRC and Saudi Arabia. Some of Indonesian products that have entered Djibouti market and quite in demand are food and beverages products, cars, chemicals and petroleum products. In fact, Sarong products from Indonesia have been well-known and loved by Djiboutian.  

In 2015, Indonesian Embassy in Addis Ababa has accompany 20 people from Chambre de Commerce de Djibouti (CCD) headed by the President of CCD, Youssuf Moussa Dawaleh. In between visits to TEI 2015, CCD delegation has met with KADIN Indonesia (Indonesian Chamber of Commerce). CCD delegation was received by the Chairman of KADIN, Suryo B. Sulisto, the head of bilateral and multilateral KADIN for Africa and staff. In the meeting, an MoU has been signed between the two chambers to support the enhancement of cooperation and facilitation of visits from the members of the two chambers.  

In 2016, CCD headed by Youssuf Moussa Dawaleh, once again visits TEI 2016 and brought 30 entrepreneurs. 

During Indonesia Africa Forum in Bali April 2018, Pelindo II and Djibouti Ports and Free Zones Authority (DPFZA) has signed an MoU marking the beginning of cooperation between the two ports on 10 April 2018. The MoU was signed by Director of Operation and Information Systems from Pelindo II, Prasetyadi and Administrative Director from DPFZA, Mohamed Aden Cheikh. 

The focus of the MoU is to develop technology, to improve operations, customer services, and mutual cooperation in maritime business and trade. Moreover, with the MoU, both ports will share information and policies on training of personals, field practice, comparative study, operational improvements, with the aim to increase trade and maritime services. 

Also at the Indonesia Africa Forum, the KADIN Indonesia headed by Rosan Perkasa and CCD headed by Youssuf Moussa Dawaleh have discussed the possibility of cooperation between the two chambers in the field of trade and Free Zone Area in Djibouti on 11 April 2018. In addition, still on the same day, PT Wika Indonesia also signed an MoU with Dawaleh Construction to build housing in Djibouti.