The fiscal year of the District is from July 1st to June 30th inclusive. Each year, the BBHD Board of Health has a public hearing on its proposed budget. Following the public hearing and before April 30th of each year, the Board adopts its annual budget in accordance with its estimate of financial requirements for the next fiscal year. An annual audit of the finances of the District is conducted in the fall. The District receives federal, state and local funds. In addition to funding for public health emergency planning and prevention programs from the federal government, BBHD is funded on a per capita basis formula from the State of Connecticut. A proportionate share of the expenses of the District, to pay the cost of operating the District, is established using the last annual population estimate for the State of Connecticut Department of Public Health, for each participating town or city.

For fiscal year 2008, the District received $6.62 per capita from the City of Bristol and Town of Burlington and $2.08 per capita from the State of Connecticut. Additional fees are generated through the issuance of permits and licenses.