Objectives <p>Impedance pneumography (IP) records respiratory cycle and provides non-invasive means to evaluate changes after thoracic surgery. This comparative study evaluated if changes after thoracic surgery can be modified by two pulmonary rehabilitation modalities.</p> Methods <p>88 patients undergoing thoracic surgery were randomly allocated to either positive expiratory pressure (PEP) or inspiratory muscle training (IMT) physiotherapy group. Physiotherapy was performed and IP recorded preoperatively and at first and second postoperative days (POD1 and POD2) during tidal breathing. Full three timepoint IP data were collected from 81 patients (42 in the PEP group, 39 in the IMT group). Average inspiration and expiration time in seconds (TinspAvg and TexpAvg) and average breathing frequencies (BrthFreqAvg) were calculated from a 10-min measurement period and assessed as primary outcomes. Results were also assessed in blocks of different surgical techniques (thoracotomy or VATS) and the extent of surgery (pulmonary resection or minor thoracic operation).</p> Results <p>TinspAvg and TexpAvg decreased after surgery but started to increase in the IMT group between POD1 and POD2 with no significant difference compared to PEP group. Among patients operated with thoracotomy TexpAvg was slightly but insignificantly higher in the IMT group at POD2. The ratio between the time of expiration and the time of inspiration (EI ratio) was significantly higher in the IMT group with thoracotomy (difference between groups over three timepoints, (<i>p</i> = 0.044) and at POD1 (<i>p</i> = 0.015)).</p> Conclusions <p>IMT seemed to enhance expiration specifically among thoracotomy patients and thus may provide means for enhancing the recovery after thoracic operations.</p> Clinical trial registration <p>NCT02931617/U.S. National Library of Medicine, ClinicalTrials.gov.</p>