The van had been working with families around bombed-out streets in the Palestinian territory for 17 years, thanks to funding from the Church in Wales.
Lead Bishop, John Davies, the Bishop of Swansea and Brecon, said: "We would like to thank everyone who contributed over the years."
The mobile dental unit was operated by the Near East Council of Churches as part of the work of its family health centres in Gaza.
It has now been decided the work of the van will become part of the overall work of the centres and, thus, funding for the vehicle is being wound up.
Bishop John went on to say: "We are pleased that the Church in Wales was able to respond to the call for practical help when it was most needed and we are proud to have been able to fund the mobile clinic for so long.
"The van, with its Welsh red-dragon stickers, was a familiar sight in Gaza City, and examinations, treatments and medicines were provided free of charge, thanks to the generosity of churches and individuals in Wales.
The mobile dental unit in Gaza was the main beneficiary of the Church in Wales' Jubilee Fund, created to mark the new millennium and to support good causes around the world.
The fund has raised nearly £220,000 and supported eleven overseas projects.
Bishop John added: "The Jubilee Fund was originally set up with an expected ten year life span.
"Having achieved its primary objectives in the first decade, due to events in Gaza in 2008-09 and the continuing work of the mobile dental unit, the Bishops decided to extend the funding."