The 44-year-old from western Sydney is the first to be charged since a special anti-Semitism task force was formed following the firebombing of a synagogue.
Police say the Blacktown man posted death threats on a Jewish association's social media page.
He was charged with one count each of using a carriage service to make a threat to kill and using a carriage service to menace, harass or cause offence.
AFP Assistant Commissioner Stephen Nutt said anti-Semites should be on notice. (Mick Tsikas/AAP PHOTOS)
"It is abhorrent that individuals are being targeted and threatened because of their race or religion," Australian Federal Police Counter Terrorism and Special Investigations Command Assistant Commissioner Stephen Nutt said on Thursday.
"Anti-Semites should be on notice.Â
"If you engage in anti-Semitic conduct, you will investigated and prosecuted to the full extent of the law."
The man was granted police bail and is scheduled to appear in Downing Centre Local Court on February 26.
The offences he has been charged with carry a maximum penalty of 10 and five years' imprisonment, respectively.
Special Operation Avalite, which is led by specialists from the Australian Federal Police and the Australian Security Intelligence Organisation, was set up in December following the arson at Melbourne's Adass Israel Synagogue.
It followed earlier arson attacks on cars in the Sydney suburb of Woollahra and the electorate office of Jewish Labor MP Josh Burns.
More than 20 police and analysts target high-harm and recidivist anti-Semites including those who urge violence, terrorism and genocide, or unlawfully display prohibited symbols.
Mr Nutt said a number of individuals were under investigation and the community should expect further charges.
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