Later years of Jawaharlal Nehru consisted of him being at the helm of government. He led the congress to a major victory in the 1957 elections, but his government was facing serious problem and criticism. Disenchanted by the alleged intra-party bickering and corruption, Pandit Nehru contemplated resigning but still continued to serve in the government.

The election of his daughter Indira as President of Indian National Congress in the year 1959 aroused criticism for alleged nepotism, although in reality Nehru had condemned her election, partly because he considered it smacked of "dynastism" and refused her a position in his cabinet. Indira Gandhi herself was at loggerheads with her father over policy; most notably, she used his oft-stated personal deference to the Congress Working Committee to push through the dismissal of the Communist Party of Government of India in the Indian state of Kerala, over his own objections. Jawaharlal Nehru actually began to be frequently mortified by her ruthlessness and disregard for parliamentary convention, and was "hurt" by what he saw as assertiveness with no purpose other than to stake out an identity independent of her father. In the 1962 elections, Nehru led the Congress to victory yet with a diminished majority. Communist of India and other socialist parties were the main beneficiaries although some right wing groups like Bharatiya Jana Sangh also did well.

Nehru`s health, after 1962, steadily started to decline and he spent months recovering in Jammu and Kashmir through 1963. Some historians attribute this dramatic decline to his surprise and chagrin over the Sino-Indian War, which he perceived as a betrayal of trust. Upon his return from Kashmir in May 1964, Nehru suffered a stroke and later a heart attack. He was "taken ill in early hours" of 27 May 1964 and died in "early afternoon" on same day, and his death was announced to Lok Sabha at 1400 local time; cause of death is believed to be heart attack. Nehru was cremated in accordance with Hindu rites at the Shantivana on the banks of the Yamuna River, witnessed by hundreds of thousands of mourners who had flocked into the streets of Delhi and the cremation grounds.

Jawaharlal Nehru, the man and politician made such a powerful imprint on India that his death on 27 May 1964, left India with no clear political heir to his leadership (although his daughter was widely expected to succeed him before she turned it down in favour of Shastri). Indian English newspapers repeated Nehru`s own words of the time of Mahatma Gandhi`s assassination: "The light has gone out of our lives and there is darkness everywhere."