Background Sturge-Weber syndrome (SWS) is a rare condition associated with a GNAQ gene mutation, which affects neural crest cells. A pulsed dye laser (PDL) is a first-line therapy for SWS, but its outcomes are worse than those in patients with port-wine stains (PWS). Photodynamic therapy (PDT) is a promising therapeutic option for PWS. However, its use for PWS associated with SWS has rarely been studied. Aims To investigate the therapeutic and adverse effects of photodynamic therapy in treating SWS-associated PWS. Methods Patients with SWS and matched patients with large size facial PWS were included in this study. Both colorimetric assessment and visual evaluation were conducted to evaluate patients' responses to treatment. Results Colorimetric assessment (blanching rate) and visual evaluation (scores of colour improvement) showed that after two PDT treatments, the SWS and PWS groups had similar treatment responses (21.2% vs. 29.8%; 3.39 vs. 3.65; P = 0.18, P = 0.37). However, there was a significant difference in efficacy between patients with SWS with and without a treatment history (12.4 and 34.9%, respectively; P = 0.02), as well as between patients with lesions located on the central and lateral faces (18.5 and 36.8%, respectively; P = 0.01). Both the SWS and PWS groups experienced minor adverse effects, and the frequency of these effects was not significantly different between the two groups. Limitation The study was limited by a small sample size and the possibility of later onset of glaucoma. In addition, false-negative magnetic resonance imaging screening results for SWS could not be ruled out due to the young age of some participants. Conclusion Photodynamic therapy is a safe and effective therapeutic option for SWS-associated PWS. Patients without a treatment history, and lesions on the lateral face, responded well, demonstrating good efficacy.