The Operations Unit manages all logistical aspects of refugee movements from camps to their final countries of resettlement. Since 2007 through August 2024, the unit has facilitated the resettlement of over 113,722 Bhutanese refugees to Australia, Canada, New Zealand, Norway, Denmark, the Netherlands, the United Kingdom, and the United States.

In Nepal, the Operations Unit is responsible for transporting Bhutanese refugees from camps to IOM offices for interviews and medical appointments. The team also coordinates flights from Eastern Nepal to Kathmandu. Upon arrival in Kathmandu, the Operations team provides accommodation for refugees at a nearby hotel for two days before their international departure.

The Unit manages international airline bookings and oversees all airport formalities for departing refugees. The Unit also arranges operational flight escorts as needed and provides medical escorts in coordination with the Migration Health Unit for medical cases. Additionally, the Operations Unit handles flight movements for cases originating from Sri Lanka and India.