"Had a positive meeting reviewing the gamut of our partnership," PM Modi said at a joint press event with Deuba and assured him of India's commitment towards overall growth and development of the Himalayan nation.
Mr Deuba said Nepal would "never allow any anti-India activities from its soil".
The two leaders also jointly inaugurated the Kataiya-Kusaha and Raxaul-Parwanipur cross border power transmission lines.
PM Modi identified defence and security as an important aspect of bilateral ties.
Earlier, Mr Deuba was accorded a ceremonial welcome at Rashtrapati Bhavan, where he is staying as a state guest. Mr Deuba arrived in New Delhi yesterday on a four-day visit, his first foreign trip after assuming office in June this year.