The clinic says women have been unable to pay for the procedure and its revenues have never met expenses.
It says it cannot continue to provide services that are not publicly funded.
Abortion isn't covered by medicare in New Brunswick unless two doctors certify in writing that it is medically necessary and is performed by a specialist in an approved hospital.
The Morgentaler clinic charged between $700 and $850 for the procedure, depending on how far along a woman is in her pregnancy.
In 2002, Dr. Henry Morgentaler launched a lawsuit to force the provincial government to pay for the procedure.
The case has been in limbo since Morgentaler died last May.
Morgentaler was a family doctor in Montreal in 1967 when he emerged as an advocate for the right of women to have abortions on demand.