The two-day visit comes just three weeks after Rice's last trip to the region.
Palestinians say that Israel is undermining Mahmoud Abbas, the president, in his struggle with Hamas by failing to remove restrictions on movement.
But Israel contends that checkpoints, which are stifling the Palestinian economy, are necessary to keep out suicide bombers.
"Obviously, there are security issues but we do have to find ways to improve movement," Rice said during her flight to the region.
"There are obstacles that are not checkpoints and there are checkpoints that are obstacles. I think you need to look at both."
Peace talks between Israel and the Palestinians were officially relaunched at a US-hosted peace conference in November, where Abbas and Ehud Olmert, the Israeli prime minister, pledged to try to reach a peace accord this year.
Peace efforts have been compromised by an upsurge in Israeli military operations against Palestinian fighters in the Gaza Strip and continued Israeli construction in areas Palestinians claim for a future state.
Rice usually meets the two sides separately, but in a possible sign of the urgency assigned to the visit, she is to meet Salam Fayyad, the Palestinian prime minister, and Ehud Barak, Israeli defence minister, together.
Rice will also hold a joint session with Tzipi Livni, Israeli foreign minister, and Ahmed Qureia, the chief Palestinian negotiator.
On the ground, meanwhile, two Palestinians were killed in Israeli air strikes in east Jabaliya in Gaza on Saturday.
Palestinian medical sources said medical crews were searching for bodies of the two men after co-ordination with the Israeli side.
They have not yet been identified.