Background: HER2 expression is an adverse prognostic factor of bladder urothelial carcinoma (UBC) while the prognostic value of HER2 expression in upper tract urothelial carcinoma (UTUC) remains to be explored. This study aims to investigate the prognostic value of different HER2 expression and gene amplification levels in UTUC. Methods: The baseline clinicopathological data of 130 patients with UTUC were reviewed. The expression level of HER2 was detected by immunohistochemistry (IHC) staining (Anti-Her2/neu, Cat.4B5, Ventana) from formalin-fixed paraffin-embedded (FFPE) tumor tissue of patients. The HER2 gene amplification level was detected by second-generation sequencing (NGS) (HER2 gene copy number [CN]) or Fluorescence in situ hybridization (FISH) from FFPE tumor tissue of patients. HER2 negative was defined as IHC 0. HER2 low expression was defined as IHC 2+ but CN- or FISH-, while HER2 overexpression included IHC 3+, and IHC 2+ but CN+ or FISH+. The correlation between HER2 expression levels or other clinicopathological characteristics and overall survival (OS) were analyzed. The Cox proportional-hazards model was used to analyze the independent prognostic factors of UTUC. Results: All the 130 patients provided FFPE tumor slides for the IHC detection of the HER2 expression levels including: IHC 0 (n = 47), IHC 1+ (n = 28), IHC 2+ (n = 41) and IHC 3+ (n = 14), the median OS were 27.5 months, 48.7 months, 67.3 months, and not reached, respectively, with significantly difference (P = 0.014). Among the 41 patients with HER2 IHC 2+, 15 patients received the detection of the HER2 gene amplification level by NGS or FISH while the other 26 patients whose HER2 gene amplification levels were unknown were excluded from the analysis. The patients of HER2 negative, low expression, and overexpression had a median OS of 27.5 months, 58.0 months, and 60.0 months, respectively, but the difference was not significant (P = 0.184). Cox proportional-hazards model also verified that the HER2 IHC expression is an independent prognostic factor on the survival, while the prognostic value of the HER2 gene amplification levels was not found. Conclusions: HER2 IHC expression is an independent factor for the prognosis of patients with UTUC. However, HER2 gene amplification levels have no impact on the prognosis of UTUC patients. HER2 expression especially the HER2 gene amplification level in UTUC needs to be explored further.