Abstract Background The prevalence of major depressive disorder (MDD) in women is up to 50% higher as compared to men. However, little is known about discrepancies in health care utilization between depressed female and male patients. Consequently, the aim of the present study was to elucidate gender differences regarding the frequency of hospital admissions and the length of inpatient treatment for MDD across the lifespan. Methods This nationwide, registry-based study analyzed all inpatient admissions in psychiatric hospitals due to recurrent/non-recurrent MDD episodes according to ICD-10 (moderate (F32/33.1), severe (F32/33.2), severe with psychotic features (F32/33.3)) in Austria across 14 years. We calculated weekly admission rates per 100,000 patients by directly age-standardized rates. Results Across 232,289 admissions (63.2% female) the population based admission rates in MDD were significantly higher in women (p < 0.001). Female to male ratios across subgroups were 1.65 (F32/33.1), 1.58 (F32/33.2), 1.73 (F32/33.3), and peaked around 65 years (ratio ≥ 2 for all subgroups). Length of hospital stay for women was significantly longer in all depression subtypes (p < 0.001). Conclusions Elevated rates of inpatient treatment in women cannot solely be explained by a higher MDD prevalence and are dependent on age and type of depressive episode. Irrespective of the type and severity of the mood episode, women exhibit longer hospitalisation times.