The first use of the word Malla in the Kathmandu Valley begins from 1201. It is believed that Ari Dev, first monarch of Malla dynasty, was extremely passionate about the wrestling, and one day while he was wrestling got information about the birth of his son and then after he decided to use Malla as his surname. The first son of Ari Dev Malla was Avaya Malla.

The Malla Dynasty was the ruling dynasty of Kathmandu Valley, from the 12th to the 18th century. The Malla period was a golden one that stretched over 600 years, as they presided over and flourished the Newa civilization of Nepal Mandala which developed as one of the most sophisticated urban civilization in the Himalayan foothills. In those days, the Kathmandu Valley and surrounding region was known as Nepal or Nepal Mandala. In the late 15th century, Yakshya Malla (1428–1482) divided Nepal Mandal into three kingdoms Bhaktapur, Kantipur and Lalitpur.  After demise of Yakshya Malla, Bhaktapur was ruled by his eldest son Raya Malla (1482–1504) and Kantipur by Ratna Malla. Bhuwan Malla (also known as Subarna Malla) (1505–1519) was the son of Raya Mall who ruled Bhaktapur after the demise of Raya Malla. Bhuwan Malla had three sons Pran Malla, Jitmitra Malla and Purna Singh. After Bhuwan Malla, Pran Malla (1519–1522) became the king of Bhaktapur. The second son Jitmitra Malla had no issue. The youngest son of Bhuwan Malla was Purna Singh. Mr. Devendra Kumar Mall compiled the decedent of Purna Singh in the form of a booklet and he gave the title to this book as “Bhaktapur ka Raja Bhuwan Malla Ko Bamsaj” (भक्तपुरका राजा भुवन मल्लको वंशज.) and published by Amriteshar Lal Malla. The book contains 1124 names of Malla family from 13 districts of Nepal.

On Falgun 16, 2055 BS, the Book was launched at Hotel Mountain, Kantipath, in presence respectable dignitaries of Malla (Pradhananga) family by first mining engineer of Nepal Mr. Puspa Bhakta Malla. The book launching ceremony was presided by Prof. Aishwarya Lal Pradhanaga, an eminent economics and former minister of Government of Nepal. The huge gathering on that day suggested to form an organization. An ad-hok committee was formed on the leadership of Prof. Aishworya Lal Pradhananga which drafted a regulation of Malla (Pradhananga) Pratisthan. Later 11 members executive committee was elected. The first executive committee consists of Prof. Aishworya Lal Pradhananga, Chairman, Mr. Devendra Kumar Malla, the Vice chairman, Mr. Amriteshwor Lal Malla the General secretory, Mr. Shashi Sundar Malla the treasurer. The other members of Malla (Pradhananga) Pratisthan were Mr. Mahendral Lal Pradhanaga, Mr. Madhab Sundar Malla, Mr. Nripendra Kumar Malla, Dr. Raja Ram Pradhananga, and Mr. Tara Chandra Pradhananga.

Even during the Malla rule, many decedents of Malla dynasty used Pradhananga (chief of the chiefs) in lieu of Malla. It is still not clear whether Pradhananga is just the title of the job that was assigned or the surname used by Malla decedent because of various reasons. One can find lots of Pradhananga, the direct decedents form Malla dynasty, in different places of Bhaktapur, Nakadesh, Tharpu and many other places of Nepal. Owing to this the name of our organization is given the name Malla (Pradhananga) Pratisthan. Many Pradhananga these days revert back to write Malla as their surname.

The executive committee of Malla (Pradhananga) Pratisthan is periodically elected by the assembly of members of Pratisthan. At present Dr. Madhab Malla is the chairman of the Pratisthan.