Lightning damage to carbon fiber reinforced polymer (CFRP) laminates is a complex phenomenon in which thermal, electrical, and mechanical effects on the laminates occur simultaneously over a short period. Although the damage mechanism in CFRP laminates due to lightning strikes has been investigated, few studies have reported lightning damage to adhesively bonded composite structures. In this study, the effects of lightning current on the mechanical properties of adhesively bonded composite joints were evaluated. Electrically conductive adhesives were manufactured by adding an electrically conductive filler and inserting a copper mesh. The shear strength of the adhesively bonded CFRP joints was evaluated before and after the direct application of lightning current. The lightning damage caused to the adhesively bonded joints with high impedance (～40 kΩ) was found to be relatively small, and no significant reduction was found after the lightning strike tests. Conversely, the joints with low impedance (4–20 Ω) were severely damaged due to lightning currents, leading to a decrease in joint strength. The failure mechanisms are discussed herein on the basis of the observation made using high-speed photography and the results of shear strength tests.