The Boston Harbor Islands Partnership does not have its own budget; rather, it relies on the individual Partnership agencies and cooperators to fund park operations and development. Funds to carry out the park's mission are from government appropriations, philanthropy, use fees, income from commercial operations, and revenue-generating activities (such as sales of island-related products).

When the Congress created the Boston Harbor Islands national park area, it also created a new funding method. The park operates under the requirement that federal funding for the park be matched by nonfederal funding. The nonfederal share may be in the form of cash, services, or in-kind contributions. Federal funds that may be appropriated over time must equate to a ratio of one federal dollar to at least three dollars from other sources. This does not mean that there is an automatic federal contribution of one dollar for every three nonfederal dollars spent on the park. The effect of the legislation is to require nonfederal spending at Boston Harbor Islands (in contrast to traditional national parks), and limit federal support to no more than one-quarter of the total.

It is explicit in the 1996 law establishing the park that the jurisdiction of the Commonwealth of Massachusetts, or any of its political subdivisions, remains unchanged. Therefore, responsibilities to protect park resources and provide visitor services that existed prior to establishing the national park area continue as part of the partnership management of the park.

All federal monies spent in support of the park count toward the federal spending limit of one-quarter of the total. Federal appropriations are primarily through the National Park Service. Also included is U.S. Coast Guard spending for resource protection and visitor services on Little Brewster Island. Each of the other Partnership agencies, except the Advisory Council, provides the nonfederal portion of park financing. Appropriations from the Commonwealth are primarily through the Department of Conservation and Recreation budget. Public agencies are expected to fund large infrastructure projects throughout the system. Municipal support is also part of the nonfederal portion of park financing. This includes spending by the City of Boston for Rainsford Island and portions of Spectacle and Long islands.

Partnership members support each other to obtain additional financing. It is understood that new sources of revenues will not offset base level support provided by appropriations. New funding is sought through fund raising, fee retention, and revenue generation to support the mission and operation of the park, as allowed by law. The Island Alliance is the preferred vehicle for revenue generation, expenditure, and management in support of the other Partnership members. The Partnership follows the relevant regulations of the Office of Management and Budget, which cover cost and auditing principles for state, local, and Indian tribal governments, and nonprofit organizations.

Given the nature of the funding sources, no firm public commitments can be obtained in advance. Typically legislative bodies do not make long-term commitments, and no federal or state funding is set aside for the park beyond appropriations. Although anticipated funding sources may be identified in the park's five-year strategic plan, projects are initiated when funding is assured.