All three were wounded at the Shubra El-Kheyma Metro station in the northern part of the capital, Xinhua reported citing state-run Nile TV.
Other explosions were reported at Kubry al-Qupa and Ghamra stations.
Egypt has witnessed a wave of militant attacks and explosions, mainly in the restive Sinai peninsula since the ouster of Islamist president Mohamed Morsi. But the violence has spread to the capital and Nile delta cities recently.
Ansar Bayt al-Maqdis, an Al Qaeda-inspired group, claimed responsibility for most of the attacks, which they said were in retaliation for police crackdown on Morsi's supporters.
A disposal team was combing other Metro stations for possible bombs, the report said, adding the Metro system resumed operation after a halt of more than 15 minutes.