"We are not scared of the army. We are not scared to fight. We will fight," he told the pan-Arab Al-Jazeera network in an interview to be broadcast on Sunday.
Asked by the interviewer if that meant he was ready to take up arms, Malema said "Yeah, literally I mean it literally. We are not scared...
"We will run out of patience very soon and we will remove this government through a barrel of a gun".
Late last month, South Africa's constitutional court ruled Zuma had violated the constitution in using public funds to upgrade his private residence and said he must repay the money.
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EFF deputies regularly disrupt parliamentary sessions, sometimes shouting anti-Zuma slogans.
Last year, EFF MPs were expelled from the assembly by security guards after fights broke out.
"We are a very peaceful organisation, we fight our battles through peaceful means, through the courts, through parliament, through mass mobilisation, we do that peacefully," Malema told Al-Jazeera.
The EFF leader, 35, was expelled from the ruling ANC in 2012 when he was head of the party's youth wing.
A year later he founded the radical leftist EFF which entered parliament with 25 deputies after May 2014 elections, becoming the third largest party.