At the age of six he became a student at St. Joseph's Convent in Kalimpong but had to terminate his studies due to attacks of malaria. From ages eight to 11 he studied monkhood under his uncle, Rimpoche Lhatsun, and was subsequently recognized as the reincarnate leader of both Phodong and Rumtek monasteries. He continued his studies at St. Joseph's College in Darjeeling and finally graduated from Bishop Cotton School in Simla, in 1941.
He served as adviser for internal affairs for his father, Sir Tashi Namgyal, the 11th Chogyal, and led the negotiating team which established Sikkim's relationship to India after independence in 1949.
In 1950 he married Sangey Deki, daughter of an important Tibetan family, and together they had a son and daughter. Sangey died in 1957.
In 1963, at the age of 39, he married Hope Cooke, 22, an American graduate of Sarah Lawrence College in an event that brought worldwide media attention to Sikkim.
After his father's death in 1963, Prince Palden was crowned the new Chogyal on an astrologically favorable date in 1965.
India annexed Sikkim in 1975, ending Palden Thondup Namgyal's rule.
On January 29, 1982 Palden died of cancer in New York. Although sworn to uphold the Indian Constitution, 31 members of the State Legislative Assembly offered khadas to the Chogyal upon his death, showing that many Sikkimese still regarded the Chogyal as their actual ruler.
His son from his first marriage, Wangchuk Namgyal, was named the 13th Chogyal, but the position no longer confers any official authority.