Idress Kamal, the head of an anti-militancy civil society group that has taken up Afridi's case, said an appeal had been filed in a court in Peshawar against the doctor's conviction.
The appeal also challenges the sentence and charges levelled against Afridi, he said.
Afridi was arrested days after bin Laden was killed in a unilateral American raid in the garrison town of Abbottabad on May 2 last year.
Though he was accused of assisting the CIA track bin Laden through a fake vaccination campaign, he was convicted of helping and funding the banned Lashkar-e-Islam militant group by a tribal court on May 24.
The tribal court said it did not have the jurisdiction to take up charges that Afridi had worked for the CIA.
Kamal said the appeal was filed in a court in Peshawar that hears appeals against judgements given by tribal courts under the British-era Frontier Crimes Regulation. "All the charges labelled against him were baseless. Shakeel Afridi had no links with Lashkar-e-Islam," he said.
Significantly, the Lashkar-e-Islam, which is led by commander Mangal Bagh Afridi, has denied any links with the doctor.
A spokesman for the banned group even threatened to kill Afridi.
Afridi's conviction and sentencing has angered the United States, which has called for his release.