The agreement to establish the consultations was signed in the presence of Kovind and his Djiboutian counterpart Omar Guelleh.
Kovind thanked Guelleh for his country's support during Operation Rahat for evacuating Indians from war-torn Yemen in 2015, and also discussed cooperation in the maritime and renewable energy domains.
He also urged for an early ratification of Djibouti's membership of the International Solar Alliance and mentioned its solar energy potential.
Earlier today, Kovind was accorded a ceremonial welcome by Guelleh at the Presidential Palace here before leading delegation-level talks.
He is the first Indian leader to visit Djibouti.