Hybrid polymer composites are used in many secondary load carrying structures and use of natural fibers for hybridization is one of the options. However, in view of the higher levels of mismatch in strength between synthetic fibers and natural fibers, the failure modes of hybrid natural fiber composites are different. Advanced non-destructive test methods such as infra-red thermography are employed for damage detection. The present paper discusses the detection of damage in hybrid natural fiber composite laminates using active thermography method. Carbon and Flax fiber reinforcements are considered for this study. Specimens of hybrid composites prepared by hand lay-up technique were subjected to impact loading and post-impact fatigue loading to study damage progression through infra-red thermography. The laminates are tested for cooling response under transmission mode and reflection mode of thermal imaging for the test conditions of pristine specimen, impact damaged specimen, and fatigue cycled specimen after impact damage. It is observed that there is a secondary heating of specimens near the impact damaged zone when the active thermography is done in the transmission mode; the de-lamination defect can be more easily detected when the heating is from the damaged side and the measurement is from the opposite side using transmission mode. © 2017 Author(s).