St Agatha's Church is a small church in Rabat, Malta dedicated to Saint Agatha.

According to tradition, St Agatha fled from Sicily to Malta to escape persecution by the Roman Emperor Decius.

She was later brought back to Sicily when the Quintanius, the governor of Catania, her birthplace, decided that he wanted her to be his wife. She angered him by refusing him and then was tortured to death for refusing to give up her Christian faith.

A church was built on the site in 1504. This church was rebuilt in 1670.

St Agatha's church has a crypt that is cut into live rock. Legend says that St Agatha once prayed here. This crypt was a natural cave that was enlarged in the 4th and 5th centuries. The main altar at the far end of the crypt was used for worship as late as 1647. Frescoes decorating the crypt range from the 4th through the 15th centuries.

St Agatha's Catacombs are connected with the church. St Agatha is believed to have hid in the catacombs after she fled Sicily. Christian, Jewish, Roman and Punic families are buried here.

There is a museum associated with St Agatha's Church.

Among the items that can be seen in the museum are prehistoric fossils that have been found in the area.

There is a collection of crystals and minerals.

The museum contains an exhibition of pottery work, most of which is from the 3rd and 4th centuries BC.

There is also a collection of coins dating back to Phoenician times.

Among the many statues on display in the museum, there is a white marble torso of the Greek goddess Aphrodite, which was built around 300 BC, as well as an alabaster sculpture of St Agatha. The statue of St Agatha was donated by Bishop Lucas Buenos in the 17th century, and was placed in the crypt, on top of the main altar, in 1666. The statue can now be seen in the museum.