It was not immediately clear why Werthein stepped down or who would replace the South American country's top diplomat, who previously served as ambassador to the United States.
The announcement comes days before a key legislative election on Sunday, in which Milei's libertarian party is hoping to grow its minority presence to safeguard his strategy of steep funding cuts and austerity to improve Argentina's economy.
Local newspaper La Nacion reported that Werthein had been expected to leave office after Sunday's vote but he instead presented his resignation on Tuesday night.
Werthein held the post for close to a year, taking over from Milei's first foreign minister Diana Mondino, after she was fired for voting in favour of lifting the US embargo against Cuba at the United Nations.
His resignation comes at a sensitive time for Milei, whose popularity over success in lowering inflation has been hit by public anger over the effects of his cuts, particularly on the old and disabled, and a recent government corruption scandal.
Milei earlier this week said there would be a cabinet shake-up after the midterm elections, which face increased scrutiny after the United States signalled that its financial support of Argentina could hinge on the results.
The US Treasury has agreed a $US20 billion ($A31 billion) US. currency swap line with Argentina and signalled it is working on a further $US20 billion facility with banks and investment funds.
