Her lawyers have called the move "persecution" and say they will appeal.
The Bureau of Immigration order issued on Thursday also called for the inclusion of Sister Patricia Anne Fox in the agency's blacklist which would prohibit her from returning to the country.
It said Sister Patricia violated the terms of her missionary visa.
Justice Secretary Menardo Guevarra said Sister Patricia's deportation "is stayed pending appeal".
President Rodrigo Duterte has been hypersensitive to criticism, especially by foreigners, who he says have no right to meddle in domestic affairs.
His bloody anti-drug crackdown has left thousands of suspects dead and alarmed human rights groups and Western governments.
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