<jats:sec><jats:title>Background</jats:title><jats:p>Magnifying narrow‐band imaging (M‐NBI) and magnifying chromoendoscopy (M‐CE) enable accurate diagnosis of T1 colorectal cancer, but the diagnostic yields from combined M‐NBI and CE have not been fully analyzed. We aimed to evaluate the diagnostic yield of combining Japan NBI Expert Team (JNET) classification using M‐NBI and M‐CE.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Superficial colorectal lesions ≥10 mm removed at a Japanese tertiary cancer center between February 2016 and December 2018 were included. We analyzed the relationship between JNET classification, M‐CE findings, and histological results based on prospectively collected endoscopic and pathologic data.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>A total of 1573 lesions, including 56 superficial submucosal invasive cancers, 160 deep submucosal invasive cancers, and 81 advanced cancers (≥T2) were analyzed. The probability of deeply invasive cancer (95% confidence interval) was 1.8% (1.1–2.8), 30.1% (25.4–35.1), and 96.6% (91.5–99.1) in JNET Types 2A, 2B, and 3, respectively. The probability of deeply invasive cancer in JNET Type 2B lesions with non‐V, VL, and VH pit pattern was 4.3%, 16.6%, 76.0%, respectively (<jats:italic>P</jats:italic> < 0.001).</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>Our study showed the stratification by M‐NBI using JNET classification and the effect of additional M‐CE for JNET Type 2B lesions.</jats:p></jats:sec>