It has long been known that thunderstorms produce strong electric field fluctuations in their immediate vicinity, but it has been little recognized that these storms can also be a source of strong ULF magnetic field fluctuations (ULF; frequencies less than 5 Hz). Some characteristics of these magnetic field fluctuations were documented for a thunderstorm occurring in 1990. We now describe further measurements of these magnetic field changes for a well‐defined and comparatively intense thunderstorm that passed over the San Francisco Bay area on 8–9 September 1999. The thunderstorm is further characterized by measurements of its associated lightning by the National Lightning Detection Network. As compared with the results reported for the 1990 thunderstorm, the new measurements were made by two independent systems and more components of the magnetic field changes are measured. Given the possibility that the thunderstorm‐related ULF magnetic field changes can stimulate ULF hydromagnetic waves in the ionosphere, these measurements suggest, once again, that thunderstorms may be a source of ULF energy in the magnetosphere that can, in turn, lead to the generation of some of the ULF geomagnetic pulsations commonly observed on the ground. In addition, it may also be significant that the frequencies associated with these hydromagnetic waves in the magnetosphere are ideally suited for them to interact with some populations of the protons and ions in the radiation belts, potentially inducing them to precipitate into the atmosphere.