BackgroundWe aimed to examine the burden of intrahepatic cholangiocarcinoma (ICC) in Thailand and identify the prognostic factors for all-causes of death.MethodsWe conducted a population-based study of ICC patients admitted during 2009–2013 using the Nationwide Hospital Admission Database, the National Health Security Office (NHSO). There was an average of 1,051,146 patients/year with diagnosis of gastrointestinal diseases (GI). All patients with a diagnosis of ICC (ICD10- C221) were included from a total of 72,479 admissions from 858 hospitals. The surgical resection procedures such as the radical pancreaticoduodenectomy, subtotal and partial hepatectomy were analyzed. Data for all patients were censored 1 year post-study or death, whichever came first.ResultsA total of 34,325 patients with ICC during a 5-year study period (on average, 6865 patients/year, with the incidence rate of 14.6 per 100,000 population, per year. The ICC patients had a mean age of 63.8+/−11.6 years and 63% were males. The mean length of hospital stay was 6.4+/−7.3 days with a mean+/−SD cost of hospitalization of $595+/−$1160 USD per admission. There were 659 patients (1.9%) underwent surgical resection. The overall survival of ICC patients with surgery was significantly better than those patients without surgery. Hazard ratio of death for patients without surgery was 2.5 (95% CI of 2.3–2.7). Approximately 14% of the ICC patients died during hospitalization. The median overall survival of all patients after the first admission was 53 +/−0.6 days. From the multivariate analysis, factors related to all-causes of death were: patients’ age >60 years (OR = 1.2, 95% CI; 1.1–1.3), length of hospital stay of >7 days (OR = 1.1, 95% CI; 1.02–1.2), male (OR = 1.3, 95% CI; 1.2–1.4), living in the northern part of Thailand (OR = 1.5, 95% CI; 1.3–1.8) and presence of complications during admission (OR = 1.3, 95% CI; 1.1–1.5).ConclusionThe disease burden of patients with ICC in Thailand is significant with the incidence rate of 14.6 per 100,000 population, per year during 2009–2013 and showed high mortality rate of 14%.Electronic supplementary materialThe online version of this article (doi:10.1186/s12876-016-0565-6) contains supplementary material, which is available to authorized users.