Ellen Margrethe Løj (born 17 October 1948 in Gedesby, Denmark) is a Danish diplomat.
Between 2014 and 2016, she served as the Special Representative and Head of the United Nations Mission in South Sudan (UNMISS).
Prior to this appointment of July 2014 by United Nations Secretary-General Ban Ki-moon, Ellen Margrethe Løj served as the Ambassador to the United Nations for Denmark from 2001 until 2007.