Glassdor has a report that identifies the 25 Highest Paying Companies for Software Engineers. Top of the list is Juniper Networks with an average salary of $159,990, LinkedIn at $136,427, Yahoo! at $130,312, and Google at $127,143, full list (these are just base salaries, bonuses and stock options are extra). All top 25 companies pay above the national annual average software engineer base salary of $92,790. Below are the top 25 highest paying companies for software engineering.