<b><i>Background:</i></b> Penicillin allergy is a common problem in the management of infectious diseases. The aim of this study was to determine the impact of penicillin allergy on length of hospital stay (LOHS) among hospitalized adult patients and on in-hospital mortality at a national level. <b><i>Methods:</i></b> A retrospective cohort study of adult patients discharged from the Spanish Hospital System between 2006 and 2015 was conducted using the Minimum Basic Data Set (MBDS). We compared LOHS and in-hospital mortality of adult patients whose records contained penicillin allergy code V14.0 (International Classification of Diseases, Ninth Revision, Clinical Modification) as a secondary diagnosis, with a random sample without such a code. <b><i>Results:</i></b> We identified 981,291 admissions with code V14.0, which corresponded to 2.63% of all hospitalizations. Adults patients with a penicillin allergy label were significantly older than patients without such a label, with a median of 70 years (interquartile range [IQR]: 51–80) versus 63 years (IQR: 40–77). The proportion of women and the prevalence of infectious diseases were higher in the group with a penicillin allergy label (61.40% vs. 53.84%; 34.04% vs. 30.01%; respectively). We found a higher median Elixhauser-Van Walraven score in hospitalized patients with an allergy label. The median LOHS for hospitalizations with a penicillin allergy label (5 [IQR: 2–9]) was significantly longer than that in those without such a label (4 [IQR: 2–9]). Multivariate analysis showed an increase in LOHS due to the penicillin allergy label (odds ratio [OR] [95% confidence interval [CI]: 1.061 [1.057–1.065]) and a decrease in mortality in penicillin allergy records (OR [95% CI]: 0.834 [0.825–0.844]). <b><i>Conclusion:</i></b> In our study, the prevalence of a penicillin allergy label in hospitalized patients, using the MBDS, is low. Hospitalizations with an allergy label was associated with a longer LOHS. However, penicillin-allergic patients did not show higher mortality rates. Inaccurate reporting of penicillin allergies may have an impact on healthcare resources.