Abstract Background Human Papillomavirus (HPV) infection is a high-risk factor for many types of cancer development. The reported infectious rate in esophageal squamous cell carcinoma (ESCC) varies widely, ranging from 0% to 88.9%. It may be caused due to geographical location, sample size, and detection methods. In general, p16 expression is considered as a biomarker for HPV infection. However, the correlation between the p16 expression and HPV infectious status has been controversial. Methods Patients with ESCC underwent esophagectomy without neoadjuvant chemotherapy (NAC) from 2007 to 2021 were included. Three formalin-fixed paraffin-embedded blocks (oral side, tumor, and esophagogastric junction (EGJ)) from each surgical resected specimen were collected. p16 expression was examined by immunohistochemistry (labeling index ≥ 10% is defined as positive expression). The presence of HPV DNA was investigated by polymerase chain reaction. In addition, the anatomical distribution of HPV infection was investigated. Results A total of 158 patients with 417 samples were included. The positive expression rate of p16 was 3.6% (5/137), 19.2% (30/156) and 2.1% (3/146) in oral side, tumor, and EGJ, respectively. The HPV infectious rate was 7% (11/158), and six cases were detected in tumor site and the other 5 cases were detected in oral side or EGJ. In tumor tissue, HPV positive cases showed p16 positive, and the sensitivity and specificity for detecting HPV DNA by IHC of p16 were 100% and 84%, respectively. The HPV infection in ESCC specimens appears to be irregular. Conclusion This study is the largest sample size in Japan, demonstrating the p16 positive rate of 19.2% and HPV infectious rate of 7% in ESCC patients without NAC. IHC of p16 can be used as a screening examination for predicting HPV infection in ESCC because the false negative rate was 0%. In addition, we firstly reported the HPV infectious mapping in ESCC specimens, and it appears irregular and random.