ALK, ROS1 and NTRK fusions are involved in the tumorigenesis of various organs, including colorectal cancer. This study aims to clarify the prevalence of these fusions in colorectal cancer in the Japanese population. Immunohistochemical analysis of 1012 specimens of colorectal cancer revealed two NTRK‐positive cases (0.2%) whereas no ALK‐ or ROS1‐positive cases were identified. Reverse transcription polymerase chain reaction (RT‐PCR) detected an LMNA‐NTRK1 fusion in a case of adenosquamous carcinoma and a TPM3‐NTRK1 fusion in a case of tubular adenocarcinoma. Both NTRK1 fusion‐positive cases lacked activating mutations in KRAS and BRAF and were mismatch repair‐deficient with loss of MLH1 and PMS2 expression and MLH1 promoter methylation. Our results show that receptor tyrosine kinase fusions are rare but present in colorectal cancers in Japanese patients, with a prevalence similar to that reported in other countries.