The defect detection capabilities of pulse transient thermography and lock-in thermography were compared using equal excitation energies. A signal-to-noise ratio analysis was performed on defect images obtained by the two techniques. The test piece imaged by both techniques was a carbon fibre composite plate containing back-drilled flat-bottomed hole artificial defects of 4, 6 and 12 mm diameters at depths ranging from 0.25 to 3.5 mm. Similar limits of defect detection were found for the two techniques. Lock-in thermography phase images were found to exhibit anomalous switches between positive and negative phase values for different modulation frequencies and for different combinations of defect diameter and depth. This effect resulted in values of defect phase response that differed substantially from the one-dimensional thermal wave interpretation of lock-in thermography imaging. The consequences of this anomalous effect and its physical origins are discussed.