In this study of native Korean trilinguals we examined the effect of syntactic similarity between first (L1) and second (L2) languages on cortical activation during the processing of Japanese and English, which are, respectively, very similar to and different from Korean. Subjects had equivalent proficiency in Japanese and English. They performed auditory sentence comprehension tasks in Korean, Japanese, and English during functional MRI (fMRI). The bilateral superior temporal cortex was activated during the comprehension of three languages. The pars triangularis of the left inferior frontal gyrus (IFG) was additionally activated for L2 processing. Furthermore, the right cerebellum, the pars opercularis of the left IFG, and the posteriomedial part of the superior frontal gyrus were activated during the English tasks only. We observed significantly greater activation in the pars opercularis of the left IFG, the right cerebellum, and the right superior temporal cortex during the English than Japanese task; activation in these regions did not differ significantly between Korean and Japanese. Differential activation of the pars opercularis of the left IFG and the right cerebellum likely reflects syntactic distance and differential activation in the right superior temporal cortex may reflect the prosodic distance between English from Korean and Japanese. Furthermore, in the pars oparcularis of the left IFG and the right cerebellum, significant negative correlation between the activation and duration of exposure was observed for English, but not for Japanese. Our research supports the notion that linguistic similarity between L1 and L2 affects the cortical processing of second language.