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Introduction Inhalation injuries (IHI) are a major source of morbidity and mortality in burn patients. The purpose of this study is to evaluate short versus long duration of nebulized heparin in IHI and its effect on ventilator-free days. Methods This was a single-center retrospective analysis of adult patients with bronchoscopy-confirmed IHI admitted to a large academic medical center with an American Burn Association-verified Burn Unit between March 2013 and March 2018, who received nebulized heparin 10,000 units every four hours for three days or until the patient no longer had carbonaceous sputum, whichever is longer. Patients were excluded if they expired within 24 hours, had less than 48 hours of mechanical ventilation, or were made comfort care. The primary outcome was ventilator-free days of the first 28 days. Secondary outcomes include in-hospital mortality, length of hospitalization, baseline and day 3 lung inhalation score, reintubation, discharge disposition, and major and minor bleeding events. Baseline demographics were compared using descriptive statistics. Nominal data was compared using Chi-square test. Continuous data was analyzed using student’s t-test or Mann-Whitney U test, as appropriate. A sample size of 24 patients to be appropriately powered (β = 0.2; α = 0.05) was required to show a mean difference of 8 days on the ventilator. Results A total of 40 patients were included in the study. Eleven patients received nebulized heparin for three days or less, and 29 patients received nebulized heparin for more than three days. Patients were primarily white, middle-aged males. More patients in the short duration group had a history of never smoking (4 vs 1, p = 0.04), and patients in the long duration group had a higher grade of inhalation injury (grade 3 vs grade 2, p = 0.01). Median ventilator free days of the first 28 was 4 days for the short duration group and 6 days for the long duration group (p = 0.88). There was no significant difference in length of hospital stay (12 days vs 20 days, p = 0.12), lung injury score, incidence of ventilator associated pneumonia, or bleeding events. No major bleeding events occurred. Conclusions This study introduces the potential use of carbonaceous sputum as a clinical marker for directing therapy and using a shorter duration of therapy as compared to previous studies. There was no difference found in ventilator free days between groups, and this study affirmed the safety of using nebulized heparin for IHI.