Background Non-receptor protein tyrosine phosphatases (PTPNs) are a set of enzymes involved in the tyrosyl phosphorylation. The present study intended to clarify the associations between the expression patterns of PTPN family members and the prognosis of digestive tract cancers. Method Expression profiling of PTPN family genes in digestive tract cancers were analyzed through ONCOMINE and UALCAN. Gene ontology enrichment analysis was conducted using the DAVID database. The gene–gene interaction network was performed by GeneMANIA and the protein–protein interaction (PPI) network was built using STRING portal couple with Cytoscape. Data from The Cancer Genome Atlas (TCGA) were downloaded for validation and to explore the relationship of the PTPN expression with clinicopathological parameters and survival of digestive tract cancers. Results Most PTPN family members were associated with digestive tract cancers according to Oncomine, Ualcan and TCGA data. For esophageal carcinoma (ESCA), expression of PTPN1, PTPN4 and PTPN12 were upregulated; expression of PTPN20 was associated with poor prognosis. For stomach adenocarcinoma (STAD), expression of PTPN2, PTPN12 and PTPN22 was upregulated in cancer tissue; pathological grade was significantly correlated with PTPN3, PTPN5, PTPN7, PTPN11, PTPN13, PTPN14, PTPN18 and PTPN23; PTPN20 expression was related with both TNM stage and N stage; PTPN22 was associated with T stage and pathological grade; decreased expression of PTPN5 and PTPN13 was associated with worse overall survival of STAD, while elevated PTPN6 expression indicated better prognosis. For colon adenocarcinoma (COAD), expression of PTPN1, PTPN11, PTPN12 and PTPN13 was upregulated, while expression of PTPN18, PTPN21 and PTPN22 was decreased; expression of PTPN5, PTPN12, and PTPN14 was correlated with TNM stage and N stage; high PTPN5 or PTPN7 expression were associated with increased hazards of death. For rectum adenocarcinoma (READ), expression of PTPN12 was upregulated while PTPN21 and PTPN22 were downregulated. Conclusion Members of PTPN family were differently expressed in digestive tract cancers and matched normal tissues. Correlation were found between PTPN genes and clinicopathological parameters of patients. Expression of PTPN12 was upregulated in all of the ESCA, STAD, COAD and READ. PTPN5 was associated with the clinical features and prognosis of both STAD and COAD.