As had been the case with his father, most of Rajendra's rule was under the regency of his step-grandmother Queen Lalita Tripura Sundari Devi (died 1832) and Prime Minister Bhimsen Thapa.

Shortly afterward the youngest son of Rajendra's elder queen died, and Bhimsen Thapa was arrested on a trumped-up charge of poisoning the prince.

He decided to stay out of all the ruling activities and from 1839 to 1841, his senior wife Queen Samrajya was the de facto regent of Nepal.

In January 1843, Rajendra declared that he would rule the country only with advice and agreement of his junior queen, Rajyalakshmi, and commanded his subjects to obey her even over his own son, Surendra Bikram Shah.

Jung Bahadur's forces captured Rajendra in 1847 and brought him to Bhaktapur and later he was permitted to stay in Hanuman Dhoka Palace.

However, Jung Bahadur made sure that the ex-king Rajendra could not be consulted on any foreign and domestic affairs, and he was not permitted to leave the durbar without the consent of the king.