The relationship with Japan goes pre independence and pre World War 2 days. In 1903 former Prime Minister of Japan, Mr. Shigenobu Okuma, formed India-Japan friendship association. In 1947, after India’s independence, the association name was changed to Japan–India Economic Association.

India–Japan has stood by each other at critical moments in their history. The Japanese Government extensively supported the Indian National Army and the Indian Independence League during India's fight for independence. During the Second World War, the Japanese Imperial Army employed Netaji Subhash Chandra Bose's Indian National Army in battles against British forces. Many Indian independence movement activists escaped from British rule and stayed in Japan. The leader of the Indian Independence Movement, Rash Behari Bose created India–Japan relations. Future Prime Minister Tsuyoshi Inukai, pan-Asianist Mitsuru Tōyama and other Japanese supported the Indian Independence movement. A. M. Nair, a student from India, became an Independence Movement activist. Nair supported Netaji Subash Chandra Bose during the war and Justice Radha Binod Pal after the war.

At the International Military Tribunal for the Far East, one of the dissenting judgments in favour of Japan was made by Indian Justice Radha Binod Pal. The principled judgment of Justice Radha Binod Pal is remembered even today in Japan. This became a symbol of the perceived closeness of India and Japan.

Japan and India signed a peace treaty and established diplomatic relations on 28th April, 1952. This treaty was one of the first peace treaties Japan signed after the World War II. Ever since the establishment of diplomatic relations, the two Countries have enjoyed cordial relations.

India–Japan relations have traditionally been strong. The people of India and Japan have engaged in cultural exchanges, primarily as a result of Buddhism, which spread indirectly from India to Japan, via China and Korea. The People of India and Japan share a strong commitment to the ideals of democracy, tolerance, pluralism and open societies.

The British occupiers of India and Japan were enemies during World War II, but political relations between the two Nations have remained warm since India's independence.

The friendship between Japan and India is often referred as "Japanese-Indian Brotherhood"

Cultural exchanges between India and Japan began early in the 6th century with the introduction of Buddhism to Japan from India. The Indian monk Bodhisena arrived in Japan in 736 to spread Buddhism and performed eye-opening of the Great Buddha built in Todai-ji and remained in Japan until his death in 760. One of the most famous Japanese travelers to the Indian subcontinent was Tenjiku Tokubei (1612–1692), named after Tenjiku ("Heavenly Abode"), the Japanese name for India. Buddhism and the intrinsically-linked Indian culture had a great impact on Japanese culture, still felt today, and resulted in a natural sense of amicability between the two nations.

The Indian goddess Saraswati is known as Benzaiten in Japan, Brahma known as 'Bonten', and Yama, known as 'Enma', are also part of the traditional Japanese Buddhist pantheon.