More than 40% of patients undergoing percutaneous nephrolithotomy (PCNL) are left with residual stone fragments and often require secondary procedures. Portable CT (PCT) technology allows surgeons to obtain intraoperative cross-sectional imaging, identify and extract residual stones immediately, and thereby reduce the need for subsequent procedures. This prospective trial evaluates how incorporation of PCT during PCNL affects perioperative outcomes. We prospectively enrolled eligible patients undergoing initial PCNL for this trial (  = 60), which entailed a single intraoperative CT abdomen and ipsilateral antegrade ureteroscopy when the surgeon felt stone treatment was visually complete. If residual fragments were identified, the surgeon continued nephroscopy to find and remove them; if not, the procedure was concluded. These patients were compared with a retrospective cohort (  = 174) who underwent initial PCNL with postoperative imaging performed the following day. The two cohorts had similar demographic properties and stone characteristics, and location of percutaneous access. In the prospective arm, 50% of intraoperative PCT scans identified residual fragments, prompting continuation of surgery to remove them. This cohort had significantly higher stone-free rate (82% 36%,  < 0.01), lower rate of planned reintervention (7% 32%,  < 0.01), lower rate of urgent presentation with ureteral obstruction (0% 7%,  = 0.04), lower total CT-based effective radiation dose (8.4 mSv 14.6 mSv,  < 0.01), and shorter length of stay (2.3 days 3.5 days,  < 0.01) when compared with the retrospective cohort that did not use intraoperative PCT. Obtaining an intraoperative PCT scan during PCNL can substantially improve perioperative outcomes. Further evaluation of this modality through a randomized controlled trial is warranted. Clinical Trial Registration Number: NCT04556396.