Background: Modulator therapy restores CFTR function and has led to health benefits for persons with CF (PwCF) including lower rates of pulmonary exacerbations. It is unknown if modulators affect lung function trajectories after inpatient treatment of pulmonary exacerbations (PEx). Methods: We conducted a retrospective review of hospital encounters for PEx for subjects 6-25 years old admitted to a large tertiary care center from 2014-2021 in order to capture hospitalizations of individual PwCF before and after starting modulators. Descriptive analyses were used to characterize the population and lung function findings. Logistic regression analyses were conducted to assess the association between modulators and FEV1pp outcomes. Results: The study sample included 575 encounters representing 149 unique PwCF. Hospital encounters of PwCF taking modulator were associated with higher mean FEV1pp at baseline, midway, discharge, and follow-up assessments. Mean FEV1pp increased during inpatient treatment of APE with loss of lung function at follow-up regardless of modulator use. At follow-up, hospitalizations of PwCF taking modulators were associated with significantly higher probability of sustained improvement in FEV1pp from discharge (average treatment effect (ATE) 0.118, p<0.05). Conclusions: Hospitalizations for PwCF taking modulators were associated with higher lung function at all assessments. Inpatient treatment for PEx was associated with lung function recovery at discharge followed by loss of function at follow-up that was partially ameliorated by taking modulators.