Myelosuppression, a potential adverse reaction of nafcillin and rifampin, is rarely documented in pediatric populations. The objective of this study is to describe the incidence of myelosuppression in pediatric patients receiving nafcillin or a combination of nafcillin and rifampin therapy. This retrospective chart review identified patients who received nafcillin alone or in combination with rifampin. The primary endpoint was the incidence of myelosuppression as a composite outcome. The secondary endpoints were the incidence of thrombocytopenia, anemia, and neutropenia individually. Of 199 patients in this study, 98 received nafcillin alone. There was no difference in the rates of myelosuppression between patients receiving nafcillin alone or in combination with rifampin (p = 0.0763), and the use of combination therapy did not affect the development of neutropenia (p = 0.2764) or thrombocytopenia (p = 0.1672). Patients receiving combination therapy were more likely to be anemic at the end of therapy (odds ratio [OR] = 2.333, 95% confidence interval [CI] 0.999, 5.446). Similarly, patients receiving longer durations of nafcillin were more likely to experience anemia (OR 1.774, 95% CI 1.382, 2.370) and neutropenia (OR 1.256, 95% CI 1.024, 1.540). The use of nafcillin does not significantly affect myelosuppression in pediatric patients, although longer durations of therapy may result in increased rates of neutropenia and anemia. Combination therapy with rifampin may result in increased rates of neutropenia.