The monastery lies 45 kilometers (28 miles) east of Lhasa. Lying at the mountainside, it looks magnificent and grand. Tsong Khapa, the founder of Gelugpa, established it in 1409. A story says that when Tsong Khapa and his disciples were selecting construction site a crow pecked his hat suddenly and dropped it on the mountainside. Then the monastery was constructed there in accordance with Buddha's wish. Ganden monastery is the first Gelugpa monastery in Tibet. Its tripa, abbot of the monastery, is actually the Throne Holder of Gelugpa, which is Panchen Lama and Dalai Lama's order.

Main structures in the monastery consist of the Main Assembly Hall (Tshomchen) and Tantric colleges. The hall has 108 pillars and occupies a floor space of 1,600 square meters, capable of holding 3,500 lamas. Maitreya and Tsong Khapa are enshrined and worshiped in the hall. Left of the huge hall is a small hall, which was the numen chapel of the monastery. The chapel was built in 1416 and the fourth Panchen added gold roof to it in 1610. Behind the chapel, there is a huge stone flying here from India according to legend.

Tri Thok Khang is one of the early structures, which is the residence of Tsong Khapa and the successive tripas. Their clothing has been kept in the hall. In 1720, it was expanded and its gold roof was constructed during reign of the Seventh Dalai Lama. Dalai Lamas usually would stay here during visits.

Serdhung is a three-story building which houses Tsong Khapa's and his successors' stupas. In 1419, Tsong Khapa died and his disciples built the hall to house his tomb which was made of 900 taels of silver, equaling more than 1100 troy ounces. The thirteenth Dalai Lama changed it into gold later. More than 95 silvers tombs were built for deceased Ganden tripas.

Ganden monastery has two Tantric colleges which were both built by Tsong Khapa's disciples. Both the chanting halls of the two can hold 1,500 lamas chanting. Except for the two, there are more than 20 small chanting halls, which belong to different Khangtsens, smaller organizations than colleges. Each of them can house 200 chanting monks. Dormitories and Debating Courtyards are scattered in the monastery. Debating is an essential training method for lamas, and will be held almost every morning.

The monastery has extremely delicate and fine murals and sculptures. It also keeps an armor decorated with gems, which was worn by Emperor Qianlong and was bestowed to the monastery as an offer to Tsong Khapa. Its thangkas are special and similar with embroidery of south China. The most important and valuable arts left are the paintings of Buddha and Jataka stories drawn by the First Panchen Lama.