This study investigated the relative contributions of English morphological and vocabulary knowledge to second language (L2) reading comprehension among 100 adult Japanese English as a foreign language (EFL) learners. The study also investigated the extent to which the roles of morphological and vocabulary knowledge in L2 reading comprehension varied across proficiency levels. Hierarchical regression results indicated that morphological knowledge accounted for unique variance in L2 reading comprehension beyond vocabulary knowledge. Based on two proficiency levels (beginner and intermediate), morpheme-function knowledge was the only significant predictor of L2 reading comprehension for beginner learners. Vocabulary knowledge and morpheme-meaning knowledge were significant predictors of L2 reading comprehension for intermediate learners. The findings suggest that awareness of the syntactic properties of morphology contributes more significantly to L2 reading comprehension than vocabulary knowledge among Japanese EFL learners at the beginner level. However, its relative contribution to L2 reading may decrease as proficiency increases.