The influences of shared orthography, semantics, and phonology on bilingual cognate processing have been investigated extensively. However, mixed results have been found regarding the effects of phonological similarity on L2 cognate processing. In addition, most existing studies examining the influence of phonological similarity on cognate processing have been conducted on alphabetic scripts, in which phonology and orthography are always associated. Hence, in this study, we recruited Cantonese-Japanese bilinguals who used two logographic scripts, traditional Chinese and Japanese Kanji, to examine the influence of phonological similarity on L2 cognate lexical decision. Importantly, these scripts allow the manipulation of phonological similarity using identical characters across both languages. In addition, we examined how word frequency and L2 proficiency modulate cognate processing. Results showed that although word frequency and L2 proficiency played important roles in cognate processing, there was minimal overall influence of phonological similarity on cognate lexical decision. The latter finding suggests that theoretical models of bilingual word recognition may need to be refined to enhance our understanding of cognate processing regarding the role of phonology among diverse bilingual populations.