Some 743 whooping cough cases have been reported in the county so far this year, more than double the record 371 cases five years ago.
County health officials announced the latest figures on Wednesday, the paper reported.
Two San Diego County infants have died of whooping cough, also known as pertussis.
The California Department of Public Health says 6,257 whooping cough cases have been reported statewide, making the epidemic the largest since 1950.
Children age 6 months and younger are most susceptible to whooping cough.