Hamas confirmed the second strike was aimed at two of its local commanders in the area.
An Israeli army spokeswoman said the military had carried out both air raids on Friday, saying that the targets had been "terror operatives".
Rafah became the focus of international attention on Wednesday when tens of thousands of Palestinians poured into Egypt from the Gaza Strip to stock up on food and fuel which is in short supply due to an Israeli blockade.
The border wall was breached in a series of explosions that are believed to have been carried out by Hamas.