The Joint Hydrographic Center was funded by annual cooperative agreements from July 1999 until 31 December 2005. At that time, a five-year cooperative agreement was awarded with an ending date of 31 December 2010.

In January 2010, a Federal Funding Opportunity (FFO) was announced for the continuation of a Joint Hydrographic Center beyond 2010. After a national competition, the University of New Hampshire was selected as the recipient of a five-year award, funding the Center for the period of 1 July 2010 until December 2015. In 2015, another FFO was announced and again, after a national competition, the University of New Hampshire was selected as the recipient of a five-year award funding the Center for the period of 1 January 2016 until 31 December 2020.

In 2020, as that award period was coming to an end, another FFO was announced. Once again, the University of New Hampshire was selected to receive a five-year award to fund the Center from 1 January 2021 until 31 December 2025.
 

NOAA Ref. No: NA20NOS4000196