On September 8, 1955, Kung, along with several hundred priests and church leaders, was arrested and imprisoned. He was sentenced five years later to life imprisonment for counter-revolutionary activities.
Kung was secretly named a Cardinal in pectore in the consistory of 1979 by Pope John Paul II. The formula in pectore is used when a pope names a cardinal without announcing it publicly in order to protect the safety of the cardinal and his congregation. After he was released in 1986, he was kept under house arrest until 1988. Kung learned he was a cardinal during a private meeting with the Pope in Vatican City in 1988, and his membership in the College of Cardinals was made public in 1991. By then, he had reached 80, so he did not have the right to participate in a conclave.
He died in 2000, aged 98, from stomach cancer in Stamford, Connecticut. His funeral was held at St. John the Evangelist Church (now the Basilica of Saint John the Evangelist) in Stamford with Cardinal James Francis Stafford, President of the Pontifical Council for the Laity, presiding. Kung's body was then transported to Star of the Sea Church in San Francisco, California, for a Low Mass with Cardinal Paul Shan Kuo-hsi of Taiwan presiding. A requiem Pontifical High Mass using the Tridentine Liturgy in Latin was said the following day at Five Wounds Parish in San Jose, California, with Cardinal Shan again presiding. Kung is interred next to Dominic Tang, S.J. (Archbishop of Canton, China) at Santa Clara Mission Cemetery in Santa Clara, California.