In 1541, Lam Ngagi Wangchuck, came to Bhutan and moved to Trongsa from Thimphu.He mediated in a place above where the Trongsa Dzong now stands, he saw at night a butter lamp burning on a ridge where the Gonkhang (temple of protective deity) stands today. He took this to be the sacred place as prophesied and began mediating. He had a vision of Palden Lhamo here. In 1543, Lam Ngagi Wangchuk established a small temple and name it Mondrupde. Later, many people from the area become his disples and built small huts for themselves around the temple. The place began to look like a village and people called it Drongsar (new village). Later on, the pronunciation changed to Trongsa.
Zhabdrung Ngwang Namgyel was not able to fulfill his desire to visit this place, which had been built by his ancestor a hundred years before. Instead in 1647 he ordered the building of a Gonkhang which stands on the same spot where Ngagi Wangchuck built his temple in 1543. Zhabrung also appointed Minjur Tenps as the first Peonlop of Tzrongsa. He gradually began to expand the dzong and built the Ta Dzong (watch tower) in 1652. The whole eastern region was brought under the Drukpa rule and was governed from Trongsa Dzong.
Trongsa Dzong had been the seats of the Trongsa Poenlops who have governed the eastern region for over three hundred years. It was Trongsa Poenlop Jigme Namgyel who finally emerged as the most powerful national leader in the country. In 1907, his son Ugyen Wangchuck, was elected as the first hereditary King from his post of Trongsa Peonlop. For this reason, the heir to the throne of Bhutan is installed as Trongsa Poenlop before he is enthroned as King of Bhutan.
Trongsa Dzong is now the headquaterter of the Trongsa Dzongkha and home of the Trongsa Rabdey.