"We cannot disclose the country he left for due to security threats to his life," the relative said, asking for anonymity because he was also scared of militants.
"Militants warned him to stop pleading the case or else he and his family would face the consequences."
Lawyer Afridi represented doctor Shakil Afridi, who ran a fake vaccination campaign to try to help U.S. officials find al Qaeda chief bin laden.
Doctor Afridi was arrested after U.S. special forces killed bin Laden in May 2011 in the town of Abbottabad. The secret raid outraged Pakistan and strained relations between the allies.
Following the arrest, doctor Afridi was sentenced to 33 years in jail for membership of militant group Laskhar-e-Islam, an accusation he denies. But in August, Pakistan overturned his conviction, citing procedural errors and ordering a retrial.
Now the doctor faces murder charges relating to the death of a patient eight years ago. A judgment is expected on December 18.
Samiullah Afridi is the second member of the legal team to flee following militant threats.