The charity, more widely known by its French acronym MSF, received 56 million euros ($63 million) from EU institutions and member states last year.
"MSF announces today that we will no longer take funds from the EU and its Member States in protest at their shameful deterrence policies and their intensification of efforts to push people back from European shores," the group said in a statement.
The group singled out the EU's deal with Turkey in March to stem the biggest flow of migrants into the continent since World War II, according to AFP.
Under the deal, Turkey agreed to take back all migrants and refugees landing in the Greek islands, and to crack down on people smuggling over the Aegean Sea.
In exchange, the EU said it would resettle one Syrian refugee from camps in Turkey for every Syrian that Ankara takes back from Greece.
Turkey was also offered visa-free access, increased aid and sped up EU accession talks if it met certain conditions including changes to Ankara's anti-terrorism laws.