U.S. Secretary of State Hillary Clinton announced the development after a telephone call with Pakistani Foreign Minister Hina Rabbani Khar, the Defense Department said in a release.
Pakistan had shut down the supply routes last November after two dozen Pakistani soldiers were mistakenly killed by U.S forces in a border-area assault.
"I once again reiterated our deepest regrets for the tragic incident in Salala last November," Clinton said. "I offered our sincere condolences to the families of the Pakistani soldiers who lost their lives.
"We are sorry for the losses suffered by the Pakistani military. We are committed to working closely with Pakistan and Afghanistan to prevent this from ever happening again."
Pakistan won't charge NATO additional fees to use the routes, State Department spokeswoman Victoria Nuland told reporters at her daily briefing. She said there are "regular commercial costs" associated with use of the supply routes. It wasn't clear how much extra it has cost the past several months to ship supplies via alternate routes.
"In reopening them, we will be back at that regular commercial level," Nuland said. "There will be no additional fees to Pakistani authorities"
Clinton called it "a tangible demonstration of Pakistan's support for a secure, peaceful and prosperous Afghanistan, and our shared objectives in the region."
"This is critically important to the men and women who are fighting terrorism and extremism in Afghanistan," Clinton said.
"As I have made clear," Defense Secretary Leon Panetta said, "we remain committed to improving our partnership with Pakistan and to working closely together as our two nations confront common security challenges in the region."
Khar said only military supplies meant to equip the Afghan national security force will be allowed to pass through Pakistan into Afghanistan.
Clinton said she and Khar talked about wider issues of Afghan security, stability and reconciliation, and ongoing efforts to advance the two nations' shared interests, such as trade.
"Our countries should have a relationship that is enduring, strategic and carefully defined, and that enhances the security and prosperity of both our nations and the region," Clinton said.