Traveling under heavy security, the four trucks crossed the border into Afghanistan from Chaman in Pakistan's Balochistan province, CNN reported.
On Tuesday, Pakistan leaders decided to reopen the supply routes closed on Nov. 27, a day after coalition air forces mistakenly killed 24 Pakistani troops. The United States spent about $100 million more a month to use the alternative, less direct supply routes.
The November incident sent U.S.-Pakistan relations to an all-time low.
Talks to reopen routes hinged on two issues -- Pakistan's demand to charge more for each container moved across its border, and the country's demand the United States apologize for the November incident.
U.S. Secretary of State Hillary Clinton apologized Tuesday, saying in a statement, "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."
Until her apology, the U.S. government only expressed regret over the incident.
The U.S. military also will pay Pakistan $1.1 billion it owes as part of the deal reached to reopen the NATO supply lines, U.S. officials knowledgeable about the agreement told CNN. The money is part of the U.S. military's "coalition support funds" program, which reimburses the Pakistani military for counter-terrorism efforts.