In many low-noise applications, extracting information from the extremely noisy signal is required. This task can be accomplished by a lock-in amplifier if the frequency of the signal is known before detection. Error signal output from the physics package of the rubidium atomic clock (RbAC) is one of those noisy signals. A lock-in amplifier extracts the desired information from such a signal as the frequency of the error signal is known beforehand. The Space Applications Centre of the Indian Space Research Organisation is developing the Indian Rubidium Atomic Frequency Standard (IRAFS) for Navigation with Indian Constellation. We have developed a digital lock-in amplifier with a very high-resolution frequency control voltage for IRAFS. This paper demonstrates the digital lock-in amplifier with a novel method of combining two 12-bit digital-to-analog converters (DACs) to get higher resolution 20-bit output for precise frequency control and tuning. This design technique allows a digital lock-in amplifier to be used for high-performance RbAC for space applications as precision DACs with higher resolution are not available in space-qualified versions.