According to a statement from the French presidency, they signed an agreement on "the ambitious reform of the Defence Cooperation Treaty which unites France and Djibouti."
The accord, signed at Macron's office, governs the 1,500 French troops based in the small but strategically located East African country.
French troops have recently closed military bases in Mali and Niger following military coups in both countries, but there has never been any question of abandoning Djibouti, France's largest permanent overseas base.
The country is located opposite Yemen, near an opening to the Red Sea, where a large part of the global trade between Asia and the West passes.
The discussions had been held up by Djibouti's demands that France greatly increase the rent it pays, according to a source close to the negotiations.
The defence agreement was first signed in 1977 when the former French colony won independence, and was renewed in 2011.
But France only began to pay rent in 2003, following the opening of a US base in the country.
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