Background: Photodynamic therapy (PDT) is increasingly used in the treatment of various skin diseases. The main adverse effect in PDT treatment is pain. Each lesion is generally treated twice, and clinical experience suggests that the 2nd treatment causes more pain than the 1st and thus becomes a therapy-limiting factor. Objectives: To investigate the intrapatient variation in the experience of pain, between 1st and 2nd PDT treatments. Methods: We registered patients treated with PDT by using a mechanical visual analogue scale (VAS). Patients were tested immediately after the 1st and 2nd PDT treatments. Intrapatient comparison was made comparing 1st and 2nd treatments. Results: A total of 38 patients were included. The median VAS score increased significantly according to the Wilcoxon matched-pairs signed-ranks test (p < 0.02) from 4 after the 1st PDT (range 0–8) to 4.75 (range 1–10) after the 2nd PDT treatment. The VAS score of pain was increased in the 2nd treatment for 21 patients, remained unchanged in 6 patients and was reduced in 11 patients who reported less pain after the 2nd treatment. Patients who scored low (VAS <5) after the 1st treatment experienced an increase in mean VAS score of 1.4 at the 2nd PDT treatment. In contrast, subjects with a high VAS score (>5) after the 1st PDT had a mean decrease in the VAS score of 0.26 at the 2nd PDT treatment. The difference (p = 0.005) suggests that the pain at the 1st PDT treatment may be predictive of future pain. Conclusion: The 2nd treatment of PDT was significantly more painful than the 1st, although some patients experienced reduced pain on the 2nd treatment. The pain experienced at the 1st PDT treatment may be predictive of the pain at subsequent treatments.