The study aim was to compare clinical outcomes between patients undergoing transforaminal lumbar interbody fusion (TLIF) using percutaneous pedicle screw (PPS) and cortical bone trajectory (CBT) by a single surgeon. This was a retrospective matched-cohort study of 77 patients (mean age, 71.7 years; 56% female) who underwent TLIF using CBT or PPS. Thirty-nine consecutive patients in the CBT group and 38 patients in the PPS group were matched for age, sex, and fused levels. All CBT screws were inserted by using a three-dimensional patient-specific guide (MySpine MC, Medacta). Perioperative outcomes of operative time, estimated blood loss, numeric rating scale scores, and serum concentration of creatine kinase were compared between the 2 groups. At 1 year postoperatively, clinical outcomes and radiographic outcomes, including cage subsidence, screw loosening, and fusion rates, were compared between the 2 groups. The numeric rating scale scores on postoperative days 3 and 7 and serum creatine kinase levels on postoperative days 1 and 3 were significantly lower in the CBT group than in the PPS group (all P < 0.005). There were no significant intergroup differences in operation time and estimated blood loss. At postoperative 1 year, there were no significant differences in cage subsidence, screw loosening, and fusion rates between the CBT group and PPS group. Clinical outcomes were equivalent between the 2 groups. The CBT technique using three-dimensional patient-specific guides resulted in lower perioperative pain and quicker recovery after surgery, which suggests that CBT is a less invasive procedure than PPS.