His appeal was based on a statute granting Jews citizenship if they have performed a service for Israel.
The statute was used in the past to grant citizenship to Soviet dissidents who were not permitted to leave the Soviet Union in the 1970s and 1980s.
Pollard’s lawyer said in September that Barak had used a legal loophole to get around granting the citizenship request.
Wednesday, the court gave the government 30 days to explain its earlier refusal.