This study numerically dealt with effects of target crack width and asphaltic pavement thickness and its variation in ECT (Eddy Current Test)-based non-destructive detection for the deck through fatigue cracks in orthotropic steel bridge decks. Results of electromagnetic analysis by FEM indicated that a possible noise in induced voltage sign caused by actual asphaltic pavement thickness variation is not negligible even in thin pavement thickness (around 50 mm). Based on the result, a new type ECT probe for orthotropic steel bridge deck inspection was proposed and its performance was analytically examined.