She visited the Egyptian Red Crescent to gain an overview of the ongoing relief efforts for the sealed-off coastal strip, sources within the organisation said on Friday.
Jolie was received by the regional governor, who accompanied her on her tour.
Arab media reported that a representative of the US State Department was also present.
Jolie was then reported to have helped pack relief supplies for the Gaza Strip in a symbolic gesture, and expressed her gratitude for Egypt's efforts.
She also praised the crucial role played by volunteers and staff in the efficient distribution of relief supplies despite the numerous challenges.
In the evening, she is expected at the hospital in nearby al-Arish.
According to Egyptian sources, she plans to meet injured Palestinians from the Gaza Strip there.
Jolie was a special envoy for the United Nations Refugee Agency UNHCR for many years.
She continues to visit conflict and crisis regions around the world to draw attention to the suffering of civilians.
Rafah is the only border crossing in the Gaza Strip that does not lead directly to Israel.
The crossing was closed during the enclave's war.
Aid organisations have long been calling for it to be opened.
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