UN Member States chose the country in a second round of voting on Thursday in the General Assembly, with 192 ambassadors casting their ballots during pre-determined time slots, due to the COVID-19 pandemic.
The run-off took place one day after elections to select five new non-permanent members to serve on the Council, based on regional groupings.
In the second round, Kenya received 129 votes, and Djibouti 62.
Fifteen countries sit on the Security Council, the UN organ that maintains international peace and security.
Ten non-permanent members are elected by the General Assembly for two-year terms, with five elected each year.