System engineer salary in San Diego, CA

The average salary for a System Engineer is $128,895 per year in San Diego, CA. This figure is based on 354 salaries taken from job postings on Indeed in the past 36 months, last updated on August 15, 2026.

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System Engineer salaries in San Diego, CA typically range between a low of $83,919 and a high of $197,977 per year, depending on experience and the hiring company.

Some of the highest-paying cities for System Engineer in San Diego, CA include San Francisco, CA at $184,180 per year, San Jose, CA at $167,227 per year, and Santa Clara, CA at $160,320 per year.

Based on recent job postings on Indeed, some of the top-paying companies for System Engineer in San Diego, CA include Indotronix International Corp ($240,240 per year) and El Clasificado ($198,850 per year).

Compensation can vary based on the specific niche and level of responsibility within the field. Here is how the average System Engineer salary in San Diego, CA compares to related positions:

• Chief System Engineer: Average $189,266 per year
• Junior System Engineer: Average $101,087 per year
• Senior System Engineer: Average $146,411 per year