After the collapse of the Soviet Union, Switzerland established diplomatic relations with the Republic of Moldova in 1992.

In 2000, the Swiss Agency for Development and Cooperation opened a cooperation office at the request of the Moldovan authorities. From 2000 to 2008, the office focused mainly on humanitarian aid. Since 2005, Switzerland has also been implementing development cooperation, mainly in 3 key areas – Health, Local Development, and Economic Cooperation.

Over time, Switzerland's humanitarian assistance has included the renovation of elderly care homes and psychiatric clinics, in addition to emergency aid, providing powdered milk to social institutions.

Following Russia's war with Ukraine and the outbreak of the refugee crisis in the Republic of Moldova, Switzerland contributed humanitarian aid both through direct financial contributions and by supplementing ongoing projects.