Witnesses on Sunday said at least one missile hit an open area, while another exploded near an empty home.
Israeli military sources said the army fired into the area to protect occupation troops from attacks by Palestinian fighters.
There was no immediate word on casualties.
Israel has often raided Rafah to arrest Palestinian fighters and destroy tunnels that it says are used for smuggling in weapons from Egypt.
A Palestinian teenager who was seriously injured during an Israeli incursion into Rafah last week, died early on Sunday.
Palestinian medical sources said Saif Bar-Aun, 14, was shot in the head last week. His death brought to 4299 the overall toll since the September 2000 launch of the Intifada, including 3231 Palestinians and 927 Israelis.