The decision by the court's appeals panel ends years of efforts by Tsar Nicholas II's descendants to have authorities reclassify the killings from premeditated murder.
Prosecutors, lower courts and even the Supreme Court's main body had repeatedly rejected the appeals, saying the Romanov family had not been executed for political reasons.
On Wednesday, Pavel Odintsov, a spokesman for the court, said the court's presidium accepted the appeals of the Romanov descendants to "rehabilitate" the royal family, declaring them victims of "groundless repression."
The presidium, the Supreme Court's highest appeal panel, has the final word for legal appeals in Russia.
Nicholas II abdicated in 1917 as revolutionary fervor swept Russia, and he and his family were detained. The tsar, his wife Alexandra and their son and four daughters were fatally shot by a Bolshevik firing squad on July 17, 1918, in the basement of a merchant's house where they were held in Yekaterinburg.
German Lukyanov, a lawyer for the Romanov family, said the decision was based on law and said no politics were involved. "In the end, this will help the country. This will help Russia understand its history, help the world to see that Russia observed its own laws, help Russia in its development to become a civilized country," he said.
The remains of Nicholas II and Alexandra and three siblings were unearthed in 1991 and reburied in the imperial resting place in St. Petersburg.
Meanwhile, Nicholas' heir, Alexei, and his daughter, Grand Duchess Maria, remained missing for decades until bone shards were unearthed in 2007 in a forest outside Yekaterinburg, not far from the place where the rest of the family's mutilated remains had been scattered.
The Russian Orthodox Church made all seven of them saints in 2000.
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