The incident started around 8:30 p.m. Wednesday on Boynton Avenue, where police say they received a call about a man armed with a machete.
Police say the man was barricaded and had hostages that included two children.
Following a standoff, officers opened fire on the suspect, who was taken to the hospital where he later died.
All of the hostages were safely removed from the home and no one else was hurt.
SJPD has not provided information about the suspect or the hostages but is continuing to investigate.