The present study aimed to investigate the relationship between histopathological subtype and the probability of inguinal lymph node metastasis (ILNM) in patients with penile squamous cell carcinoma (PSCC). The clinical records of 198 consecutive patients with PSCC were analyzed retrospectively. Primary lesions were reevaluated according to the 2016 World Health Organization (WHO) histopathological classification. We retrieved the clinicopathological factors from the medical records including age, clinical lymph node stage, pathological tumor stage, lymphatic invasion, and nerve invasion. Uni- and multivariate logistic regression analyses were used to explore the risk factors of ILNM. Multivariate analyses identified clinical lymph node stage (P = 0.000), pathological tumor stage (P = 0.016), histologic grade (P = 0.000), and risk group of histological subtypes (P = 0.029) as independent predictors for ILNM. Compared with the low-risk group of PSCC subtypes, the intermediate- (HR: 3.66, 95% CI: 1.30–10.37, P = 0.021) and high-risk groups (HR: 28.74, 95% CI: 2.37–348.54, P = 0.008) were significantly associated with ILNM. In conclusion, the histopathological subtype of the primary lesion is a significant predictor for ILNM in patients with PSCC.