The court announced the ruling on February 4, upholding the extension that was first handed down in December.
The 49-year-old Whelan, who holds U.S., British, Canadian, and Irish passports, was arrested in a hotel room in Moscow in December 2018 and accused of receiving classified information.
He was charged with espionage, which carries a sentence of up to 20 years in prison. Whelan denies the charges and says he was framed.
His family said he was in Moscow at the time for a wedding.
After visiting Whelan last week, the U.S. ambassador to Russia, John Sullivan, urged Moscow to release Whelan and slammed Russian authorities for their “shameful treatment” of him.
“Despite the Russian government’s immediate claims that they caught Paul, quote ‘red-handed’ unquote, the investigators have shown no evidence. Zero. Paul’s case has gone on far too long, shielded in secrecy and hidden from view,” Sullivan said days after taking up his new post.