The Operations unit is responsible for all ground movements of refugees from camps through to the final country of resettlement by air. In Nepal, since 2007 through February 2018, the Operations unit has facilitated the departure of over 112,500 Bhutanese to Australia, Canada, New Zealand, Norway, Denmark, the Netherlands, UK and the U.S.A. The Operations team transports Bhutanese refugees daily from multiple camps to the IOM Offices for interviews and medical appointments, and also arranges weekly charter flights of refugees from Eastern Nepal to Kathmandu. In Kathmandu, the Operations team receives refugees transported through charter flights, and arranges accommodation for them at the IOM Transit Centre for several days prior to international departure. The team also arranges commercial airline bookings for refugees and facilitates airport formalities for all departing refugees. Refugees are provided operational flight escorts as needed, medical escorts for medical cases in coordination with Migration Health Unit. The Operations unit also handles flight movements for cases ex-Sri Lanka, India, and supports the Pakistan mission.

The IOM Transit Centre in Kathmandu has the capacity of accommodating 120 people a night. This 24-hour facility provides clean water, hygienic food, comfortable beds and a children's playground for the refugees. Typically, Bhutanese refugees from eastern Nepal spend 3-6 nights at the Transit Centre in Kathmandu prior to their commercial flight to the country of resettlement. During this time, refugees undergo a final fitness-to-travel examination, and a final Cultural Orientation session as a part of the transit process.