This study examined reading comprehension related to deceptively transparent (DT) words—lexical items that seem familiar but can trigger contextually inappropriate meanings—among 40 Korean 11th-grade EFL learners. Employing a within-subject, counterbalanced Latin square design that partially varied task order and text topic across participants, the study included measures of vocabulary breadth, vocabulary depth, background knowledge, the DT sentence interpretation task, and reading comprehension for two texts on different but comparable topics: a control text without DT words and a DT text containing DT words. The results indicated that (1) mean reading comprehension scores did not significantly differ between the control text and the DT text, (2) performance on the DT sentence interpretation task did not explain additional variance in DT text reading comprehension, and (3) vocabulary depth uniquely accounted for variance in DT text reading comprehension beyond vocabulary breadth. Collectively, these findings suggest that understanding DT text may be more closely linked to individual differences in vocabulary depth rather than the mere presence of DT words, although this interpretation should be considered in the context of learners’ overall reading comprehension levels and the specific conditions of the study.