The move, described by Palestinian border officials as a "humanitarian" gesture, will allow Palestinians stranded in Egypt and elsewhere, including students and sick people, to return to Gaza.
"Egyptian authorities reopened the Rafah crossing for three days only, from Saturday until Monday, and only in one direction to allow those stranded on the Egyptian side to return home," a statement said.
The Gaza Strip has been under an Israeli blockade for a decade. Palestinian militants in Gaza have fought three wars with Israel since 2008.
The Rafah crossing is Gaza's only gateway to the outside world not controlled by Israel but it has remained largely closed in recent years because of tensions between Egypt and Gaza's Islamist rulers Hamas.
Relations between the two soured after then Egyptian army chief, now President Abdel Fattah al-Sisi overthrew his Islamist predecessor Mohamed Morsi in 2013.
They have eased this year, however, and Egypt briefly opened the Rafah crossing for humanitarian cases in February and again in March.
The Gaza border authority said on Saturday that "more than 20,000 Palestinian citizens, who are considered humanitarian cases, are stuck in Gaza and desperately need to travel abroad" for treatment.