It is the first lawsuit to be allowed against Juan Carlos, 77, since he lost his total immunity when he abdicated last year, and the latest in a string of scandals to hit the Spanish monarchy.
The court "agreed to examine one of the paternity suits brought against Don Juan Carlos de Borbon," a case brought by Belgian housewife Ingrid Jeanne Sartiau, the official, who asked not to be named, told AFP.
A spokesman for the royal palace said it would make no comment on the matter.
The court dismissed a second suit brought by a man claiming to be Juan Carlos's son, Alberto Sola Jimenez, a Spanish waiter in his late 50s, the official said.
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Juan Carlos's last years on the throne saw the monarchy plunged into scandal, including a fraud investigation for which his youngest daughter Cristina has been ordered to stand trial.
He and Sartiau made headlines in Spain in 2012 when they teamed up and underwent DNA tests that they said showed there was a 91 per cent chance that they had one parent in common.