Gen Rawat met Deuba before leaving for Delhi.
He had arrived here on Monday, and had held a bilateral meeting with his Nepalese counterpart Rajendra Chhetri on Tuesday.
He also attended the Nepal Army Day celebrations as a special guest on Tuesday coinciding with the 250th anniversary of Nepal's unification.
Gen Rawat also visited Pokhara where he met with officers of the Western Division Headquarters of the Nepal Army, and paid homage at the Nepal Army War Memorial in Kathmandu.