Inherited metabolic disorders (IMDs) comprise a heterogeneous class of genetic disorders characterized by impaired biochemical functions in metabolism. However, incidences and outcomes of patients hospitalized with IMDs are largely unknown. We conducted a population‐based cohort study using nationwide in‐hospital claims data in Switzerland from 2012 to 2020. We assessed incidence rates of hospitalizations and hospital‐associated outcomes, stratified in five age groups (0–9, 10–19, 20–39, 40–59, and 60–90 years) and three types of IMDs (peptide, amine and amino acid metabolism disorders [AD], carbohydrate metabolism disorders [CD], fatty acid, and ketone body metabolism disorders [FD]). A total of 7293 hospitalizations with IMD were identified, of which 3638 had AD, 3153 CD, and 502 FD. Incidence rates for hospitalizations per 100 000 person‐years were highest under the age of 10 years across all types of IMDs (8.69 for AD, 5.73 for CD, 3.71 for FD) and decreased thereafter. In patients with AD and CD, hospitalization rates increased again in adults aged 60–90 years (7.28 for AD, 7.25 for CD), while they remained low in patients with FD (0.31). Compared to inpatients without IMD, adult IMD patients had a higher burden of hospital‐associated adverse outcomes including an increased risk of in‐hospital mortality, intensive care unit admission, mechanical ventilation, and longer length of hospital or intensive care unit stay. Incremental risk of 30‐day, 1‐year, and 2‐year hospital readmission was highest among children and adolescents with IMD.