<b><i>Background:</i></b> In gastroenteropancreatic (GEP) high-grade neuroendocrine neoplasms (H-NENs), Ki-67 threshold of 55% defines three prognosis subclasses: neuroendocrine tumor (NET) G3, neuroendocrine carcinoma (NEC) &#x3c;55%, and NEC ≥55%. We investigated whether the molecular profiling of H-NENs differs among these subcategories and evaluated potential therapeutic targets, including PD-L1. <b><i>Methods:</i></b> In GEP-NEN patients, we evaluated: (i) 55% threshold for Ki-67 labeling index for further stratifying NEC and (ii) immunoreactivity and gene mutations by immunohistochemistry and targeted next-generation sequencing (T-NGS). <b><i>Results:</i></b> Fifteen NETs G3 and 39 NECs were identified. Ki-67 labeling index was &#x3c;55% in 9 NECs and ≥55% in 30 NECs. Gene mutations by NGS (<i>TP53</i>, 32.9%; <i>KRAS</i>, 5.5%; <i>BRAF</i>, 4.1%) were detected in 46.6% NENs, significantly enriched in NEC ≥55% (76.7%) compared to NEC &#x3c;55% (55.6%) or NET (20.0%). PD-L1 staining in tumor-infiltrating lymphocytes was observed in NEC ≥55% (36.7%; <i>p</i> = 0.03). Median OS was 4.3 years in NET G3, 1.8 years in NEC &#x3c;55%, and 0.7 years in NEC ≥55% (<i>p &#x3c;</i>0.0001); it was 2.3 years with NGS wild-type, 0.7 years with ≥1 mutation (<i>p &#x3c;</i>0.0001), 0.8 years in PD-L1-positive patients, and 1.7 years in PD-L1-negative subjects (<i>p</i> = 0.0004). In multivariate analysis, only the proposed subclassification approach yielded statistically significant differences between groups (NEC &#x3c;55% vs. NET G3, HR 14.1, 95% CI 2.2–89.8, <i>p</i> = 0.005; NEC ≥55% vs. NET G3, HR 25.8, 95% CI 3.9–169, <i>p</i> = 0.0007). <b><i>Conclusions:</i></b> These findings identify NEC ≥55% as a biologically and prognostically distinct subtype and pave the way for more personalized treatment.