Kenya takes the seat designated for African countries.
The East African country polled 129 votes against Djibouti’s 62 in the second round to win the seat.
Kenya will replace South Africa in the non-permanent seat.
Niger and Tunisia are currently the other representatives of the African continent on the council.
All non-permanent members serve for two years.
Responding to Kenya’s win of the seat, President Uhuru Kenyatta said the win was a "demonstration of the country's growing profile and influence in the community of nations as a steadfast and dependable development partner".
He congratulated Djibouti for being a "worthwhile opponent" and thanked the African Union for its endorsement.
The UN organ that maintains international peace and security is made up of 15 countries.
Five permanent members and 10 non-permanent members.
The permanent members, who have the right to resolutions are China, France, Rusia, the United Kingdom, and the United States.
Ten non-permanent members are elected by the General Assembly for two-year terms, with five elected each year.
Joining the Council in January are Kenya, India, Ireland, Mexico, and Norway. They will replace Belgium, Dominican Republic, Germany, Indonesia, and South Africa.
Meanwhile, Estonia, Niger, Saint Vincent, and the Grenadines, Tunisia, and Vietnam will be members of the council till the end of 2021.