Examining influences of two participant factors, i.e., proficiency and working memory (WM), in second language (L2) sentence processing, this paper discusses how Japanese learners of English (JLEs) with distinct proficiency levels and WM capacities comprehend relative clauses in English. Reading times (RTs) were collected from intermediate and elementary levels of JLEs with different WM capacities using a self-paced reading task. The results revealed that: (1) JLEs had difficulty interpreting object relative clauses with animate antecedents; (2) JLEs at the elementary level processed the critical region in subject relative clauses with animate antecedents faster than that in object relative clauses with animate antecedents; (3) JLEs with the large WM capacity read embedded verbs faster than those with the small WM capacity; and (4) RTs of the verb region in the subject relative clause were shorter than those in the object relative clause. From these results, it is proposed that lower proficient L2 learners depend heavily on animacy information when they comprehend relative clauses though there appears evidence that JLEs also make use of structural information. Moreover, it is suggested that WM has a positive role in the L2 comprehension process, similar to findings in previous L2 processing studies.