The order provides the opening of all crossing points between the two areas, opening of all border markets to business.
The security forces at the border have been advised to adhere to the order.
Western Equatoria State closed its border following the outbreak of Ebola virus in the Democratic Republic of Congo.
Tembele Ilunga, a Congolese businessman said the opening of the order will boost business as business came to stand still following the closure of the border which led to the increase in prices of commodities.
The Western Equatoria State borders Central African Republic and Democratic Republic of Congo.