Nikita Khrushchev's anti-religious campaign was the last large-scale anti-religious campaign undertaken in the Soviet Union. It succeeded a comparatively tolerant period towards religion which had lasted from 1941 until the late 1950s. As a result, the church had grown in stature and membership, provoking concerns from the Soviet government. These concerns resulted in a new campaign of persecution. The official aim of anti-religious campaigns was to achieve the atheist society that communism envisioned.

Khrushchev had long held radical views regarding the abolition of religion, and this campaign resulted largely from his own leadership rather than from pressure in other parts of the Communist Party of the Soviet Union (CPSU). In 1932 he had been the First Moscow City Party Secretary and had demolished over 200 Eastern Orthodox churches including many that were significant heritage monuments to Russia's history. In July 1954, he was the initiator of the resolution of the Central Committee of the Communist Party of the Soviet Union (CPSU Central Committee) hostile to religion. He was not able to implement his ideas in practice until he achieved greater consolidation of his control in the late 1950s.

The anti-religious campaign of the Khrushchev era began in 1959, coinciding with the Twenty First Party Congress in the same year. It was carried out by mass closures of churches (reducing the number from 22,000 in 1959 to 13,008 in 1960 and to 7,873 by 1965), monasteries, and convents, as well as of the still-existing seminaries (pastoral courses would be banned in general). The campaign also included a restriction of parental rights for teaching religion to their children, a ban on the presence of children at church services (beginning in 1961 with the Baptists and then extended to the Orthodox in 1963), and a ban on administration of the Eucharist to children over the age of four. Khrushchev additionally banned all services held outside of church walls, renewed enforcement of the 1929 legislation banning pilgrimages, and recorded the personal identities of all adults requesting church baptisms, weddings or funerals. He also disallowed the ringing of church bells and services in daytime in some rural settings from May to the end of October under the pretext of field work requirements. Non-fulfillment of these regulations by clergy would lead to disallowance of state registration for them (which meant they could no longer do any pastoral work or liturgy at all, without special state permission). The state carried out forced retirement, arrests and prison sentences to clergymen who criticized atheism or the anti-religious campaign, who conducted Christian charity or who made religion popular by personal example.

Khrushchev claimed that communist education intends to free consciousness from religious prejudices and superstitions.

One of the first manifestations of the campaign, as had occurred in the 1920s, was the removal of practicing believers from the teaching profession. In 1959, reports appeared 'unmasking' secret believers in faculties of education. In one case a Christian student was asked how she would teach in an atheistic school system, and she replied "I'll give all answers in accordance with Marxism. What are my personal convictions is no one's business." The same article also took concern that atheist students felt that they could not win in a discussion with believers.

The press called for more aggressively atheistic curriculum at pedagogical institutions.

In 1959 a mandatory course was introduced called 'The Foundations of Scientific Atheism' in all higher learning institutions. Evolution and the origins of life began to be taught intensively in the school system beginning in 1959–1960, and all natural sciences were subordinated to the purpose of giving students a scientific-materialistic (i.e. atheistic) attitude towards nature.

Believers could be denied graduation at institutions of higher learning on account of their religion.