The rehabilitation of the North Luzon Expressway is a joint venture between the government and the private sector, for which the Manila North Tollways Corporation was granted the concession to finance, redesign, rehabilitate, expand, operate and maintain the NLEX under a Supplemental Toll Operation Agreement (STOA). The STOA was signed in April 1998 by the MNTC, the Philippine National Construction Corporation (PNCC) and the Republic of the Philippines acting through the Toll Regulatory Board (TRB). It was subsequently approved by former President Fidel V. Ramos in June 1998.

Under the STOA, all usufructuary rights, interests and privileges of PNCC were transferred to MNTC. This gives MNTC the right to collect toll fees during the concession period of 30 years so that it can continue to maintain the expressway, recover its investment, and settle the long-term loans used to finance the project.

The new NLEX uses a reasonable and internationally-accepted direct road-user fee principle for revenue collection. Unlike government infrastructure projects that are subsidized by taxes (which, in effect, makes non-users of the infrastructure pay for its services through the taxes they pay), the toll fees will only be paid by those who directly use the NLEX.

Investments for the NLEX project may only be recovered through toll fees, and not through tax revenues. This ensures that people who do not use the NLEX will not be burdened with the cost of the project. After the concession period, the project roads - plus all developments - will revert to the government at no cost.