Mr Sainju joined the civil service of Nepal in 1985 and contributed to economic policy analysis, poverty alleviation initiatives, formulation of medium-term expenditure framework and planning of trade route corridors. As the Joint Secretary in Ministry of Industry, Commerce and Supplies, he led Nepali bilateral negotiations teams on trade and transit with India, China, Bangladesh, Turkey and other neighbouring countries. He also contributed to trade negotiations with the United States, United Kingdom, and United Arab Emirates, operationalisation of SEZs, and formulation of laws, regulation and policies related to trade, transit, logistics and industry. He successfully completed transit protocol negotiations with China and negotiations on Letter of Exchange to amend the transit treaty with India. He had also served as Executive Director of Nepal Intermodal Development Board and National Project Director of Nepal-India Regional Trade and Transit Project and contributed to trade related infrastructure development and trade facilitation in Nepal.

He has several publications and studies to his credit. During this three-decade working experience in various capacities, he has gained expertise in planning, poverty alleviation, public expenditure management, trade and transit, trade facilitation, logistics infrastructure development, regional connectivity and industrial development and FDI issues.