What salary does a Chief Technology Officer earn in San Francisco? The average salary for a Chief Technology Officer (CTO) with SQL skills in San Francisco, California is $165,000. 165 Chief Technology Officer Salaries in San Francisco, CA provided anonymously by employees. The average chief technology officer (cto) salary in San Francisco, California is $166,051 or an equivalent hourly rate of $80. * Top 10 Related Jobs and Salaries Click a salary below to compare with Chief Technology Officer salaries in San Francisco, CA. Visit PayScale to research chief technology officer (cto) salaries by city, experience, skill, employer and more. Learn about salaries, benefits, salary satisfaction and where you could earn the most. CTO (Chief Technology Officer) salaries are based on responses gathered by Built In San Francisco from anonymous CTO (Chief Technology Officer) employees in San Francisco Bay Area. The average salary for a Chief Technology Officer is $121,237 per year in San Francisco, CA. This is 23% higher (+$31,588) than the average chief technology officer (cto) salary in the United States. The average salary for a Chief Technology Officer (CTO) with Project Management skills in San Francisco, California is $198,318. Salary information is updated daily. The average salary for a CTO (Chief Technology Officer) in San Francisco Bay Area is $233,958. The average salary for Chief Technology Officer jobs near San Francisco, CA is $138,619. The pay package includes retirement, health, overtime, pension, and other benefits on top of base salary. The average salary for the role of Chief Technology Officer is in San Francisco Bay Area is $180,000. In addition, they earn an average bonus of $15,410. The average salary for a Chief Technology Officer (CTO) is $162,168. Best Cities for Jobs 2020 NEW!