Kapoor, a 1990 batch Indian Foreign Service Officer, is currently India's High Commissioner in Mozambique capital Maputo.
"He is expected to take up his assignment shortly," the External Affairs Ministry said in a statement.
The appointment assumes significance as Israeli Prime Minister Benjamin Netanyahu is likely to visit India this year. Prime Minister Narendra Modi may also pay a return visit to Tel Aviv.
India's relations with Israel is on an upswing. President Pranab Mukherjee had visited Tel Aviv in October last year, becoming the first Indian Head of State to visit the Jewish nation.
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Kapoor, an MBA from IIM(A), also a has a Master's degree in International Political Economy from the London School of Economics.
In his diplomatic career of two decades, he has served in different capacities in the Indian Missions in Moscow, London, Geneva and Kiev apart from serving in the Ministry of External Affairs and the Prime Minister's Office.
He has also done a stint at the Commonwealth Secretariat in London as Political Adviser on Asia and Europe.