This study examined the effects of an approach that promotes EFL learners' critical thinking in an online EFL setting. Although recent studies have examined approaches to foster EFL learners' critical thinking, studies conducted in online settings are under-development. The participants were 31 Japanese undergraduate students enrolled in an online EFL course; their degree of critical thinking and resistance towards critical thinking were examined. First, the students' sense of classroom community was measured using the Rovai's Classroom Community Scale. Second, the frequency of using critical thinking in their English writing was observed adopting with Stapleton's rubric, and the resistance towards learning critical thinking was measured through a questionnaire. The results indicated that students could feel a sense of classroom community in online lessons as well as face-to-face settings, and improvements in critical thinking were found in students' writing regardless of the differences in their English proficiency level. A resistance towards tackling questions that required higher-order thinking was observed among low English proficiency level students compared to a face-to-face classroom setting. This study suggests that an online EFL course aiming to promote critical thinking reduce students' resistance offering both informal and formal interactive opportunities to answer questions involving higher-order thinking skills.