The minister in his message said India wants to realise the huge potential of bilateral relations with Mongolia.
"Leaving for Ulaanbaatar on a 3 day visit to Mongolia. Looking forward to further India's relations with Mongolia and strengthen security cooperation. Mongolia as an important strategic partner. India wants to realise the huge potential of bilateral relations with Mongolia," Mr Singh said in a tweet.
He will participate in the ground breaking ceremony of an oil refinery at Ulaanbaatar tomorrow, a Home Ministry spokesperson said, adding that Mr Singh will also attend a reception hosted by the Mongolian prime minister on the same day.
Mr Singh will call upon the Mongolian president on June 23, the spokesperson said.
The Home minister will also visit a Buddhist monastery and hold a meeting with his counterpart and Mongolia's minister for justice and interior affairs on Saturday.
He will also visit the headquarters of Mongolia's Border Protection Force there before returning to Delhi on June 24.
Mr Singh was to visit Mongolia late last year. However, the visit was postponed after he suffered a hairline fracture.
Prime Minister Narendra Modi had in 2015 visited Mongolia, the first ever visit by an Indian prime minister.
External Affairs Minister Sushma Swaraj was also in Mongolia in April this year where she discussed economic cooperation in infrastructure development, energy, services and information technology with her Mongolian counterpart.
The two countries also agreed to explore the possibility of launching direct air connectivity between New Delhi and Mongolian capital Ulaanbaatar.
Ms Swaraj is the first Indian foreign minister to visit the resource-rich country in 42 years.
Diplomatic relations between India and Mongolia were established on December 24, 1955. India was the first country outside the then Socialist Bloc to establish diplomatic ties with Mongolia.
India had supported Mongolia in getting the United Nations and Non-Aligned Movement (NAM) berths. Both the countries also share common concern on terrorism.