Chad Stratton was arrested and fined at a Black Lives Matter protest on July 28, 2020 at The Domain behind NSW Parliament House.
Ruby Pandolfi was fined at a transgender rights protest in Sydney's Taylor Square on October 10 that year.
They were fined for failing to comply with a public health order stipulating a person "must not participate in an outdoor public gathering of more than 20 people"Â as part of the NSW government's response to the COVID-19 pandemic.
"Both Mr Stratton and Ms Pandolfi were arrested in the course of engaging in outdoor protest activity which involved a gathering of more than 20 people," court papers read.
The pair challenged the fines but Supreme Court Justice Anna Mitchelmore ruled they do not have a case on Thursday.
The Public Health Act the fines were issued under "does not impose an unjustified burden on the implied freedom" of political communication, she said.
"It follows that the Penalty Notices are valid and the Summons must be dismissed," she wrote in her published reasons.
The pair challenged the penalty notices and sought to establish they were invalid under two sections of the health act.
"The plaintiffs have not succeeded in either respect," Justice Mitchelmore wrote.
She dismissed the summons, making no order on costs after noting an agreement had been reached between the parties.
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