Several protesters were wounded as Egyptian police opened fire in the air and used batons and water canons to push back the protesters.
The demonstrations on Tuesday came as Israel allowed a few fuel trucks into Gaza, easing the punishing blockade of the Hamas-run territory.
Rafah is the only border crossing out of the Gaza Strip that bypasses Israel.
Some angry protesters complained that Gaza was under siege from both Israel and neighbouring Arabs.
Al Jazeera English - News - Angry Gazans Storm Rafah Crossing