In 1991 Hungary became a member state of IOM, and the following year the organization established its office in Budapest. Since the signature of the agreement between IOM and the Government of Hungary (7 April 1992), the IOM Mission has enjoyed diplomatic status. Since then IOM has managed numerous projects in the fields of counter-trafficking, migration and health, labour migration and integration, assisted voluntary return and assistance to migrants in transit, and ran several public information campaigns on migration issues in Hungary and participated in various research activities.

The IOM office in Hungary continues to be actively involved in building the Government of Hungary's capacity to manage migration issues through training, and organizing regional and international exchange programmes, conferences and research projects. IOM Budapest has also established partnerships with a number of relevant non-governmental organizations that assist migrants and victims of trafficking in Hungary.

From November 2000 to July 2011, IOM Budapest functioned as a “Mission with Regional Functions” (MRF). First providing direct support, supervision, and assistance to IOM’s missions in the Central European region, the regional functions of the office in Budapest were then expanded to include IOM missions in South-Eastern Europe. MRF Budapest therefore not only ensured the effective sharing of core resources and expertise between the Field Offices under its responsibility but also a consistent approach in important areas such as project development and the application of administrative and operational policies and procedures throughout the Organization.

Since 2011, IOM Budapest has been the Country Mission for Hungary.

Since 2016, IOM is part of the United Nations System as the leading inter-governmental organization promoting humane and orderly migration for the benefit of all.

IOM Hungary currently has the following Units: Programme Support Unit, Resource Management Unit, Ukraine Response Unit, Labour Mobility and Social Inclusion Unit and Direct Assistance Unit.