This study’s aim is to investigate further into the relationship between individual differences—working memory and sound recognition ability—and sentence processing of Japanese scrambled sentences for second language (L2) Japanese learners. L2 Japanese learners drawn from 3rd year college-level courses or above were tested on their listening comprehension accuracy in identifying case marking particles in canonical and scrambled sentences. Participants demonstrated a significant slowdown in reaction time and low accuracy rates for scrambled sentences compared with canonical sentences. In addition, even participants with high working memory and proficiency had difficulty in comprehending scrambled sentences and could not process case markings efficiently and accurately in a timed setting. This study is significant in that it is one of the first to examine the relationship between individual differences and comprehending Japanese case markings.