This paper discusses the problem of program execution time measurement. Program execution time measurement is problematic because the conventional measurement method, based on the real-time clock interrupt counting, is prone to inherent errors. These errors are caused by discrete nature of real-time clock interrupts and by the overhead of clock interrupt processing. Ways of reducing relative magnitude of these errors are described. The program execution time measurement and error estimation are illustrated by the measurement of real-time kernel operations' execution time on the Intel 80386 EX micro-controller.