Justice Shaukat Aziz Siddiqui of the Islamabad High Court (IHC) ordered after hearing a petition by Karim Khan whose relatives, including his son Zahinullah and brother Asif Iqbal, and other civilians were killed in the drone attack on December 31, 2009.
Khan had earlier filed an application in the IHC in 2010, seeking registration of an FIR against former CIA station chief Jonathan Banks.
Khan said that registration of case would strain ties with the US, Dawn reported.
He also said the Foreign Office was also a party in the matter and it was important to know its stance.
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But the court rejected the argument and asked Khan to register the FIR with Islamabad's Secretariat Police Station and submit a report to the court within two days.
The police station had earlier refused the request to register the FIR.
In October 2014, a high court bench summoned the Secretariat police station house officer (SHO) for not registering a case against Banks.