The group said in a statement that Ismail Haniyeh left Friday, two days after Egypt opened the crossing temporarily.
It said the visit aims to discuss Gaza’s economic crisis “that put Gaza on the edge of the abyss.”
Talks will also cover obstacles stalling a Palestinian unity deal with the Palestinian government in the West Bank, it said.
To the frustration of thousands of Palestinians wishing to leave Gaza, Egypt shut the frontier after the Hamas delegation crossed and its military began an anti-insurgent operation nearby.
Egypt has kept Rafah mostly closed since Hamas took over Gaza in 2007.