The treatment of chronic pelvic pain (CPP) with botulinum neurotoxin type A (BoNT/A) has increased lately, but more studies assessing its effect are needed. This study aimed to evaluate the evolution of patients after BoNT/A infiltration and identify potential responders to treatment. Twenty-four women with CPP associated with dyspareunia were treated with 90 units of BoNT/A injected into their pelvic floor muscle (PFM). Clinical status and PFM activity were monitored in a previous visit (PV) and 12 and 24 weeks after the infiltration (W12, W24) by validated clinical questionnaires and surface electromyography (sEMG). The influence of patients’ characteristics on the reduction in pain at W12 and W24 was also assessed. After treatment, pain scores and the impact of symptoms on quality of life dropped significantly, sexual function improved and sEMG signal amplitude decreased on both sides of the PFM with no adverse events. Headaches and bilateral pelvic pain were risk factors for a smaller pain improvement at W24, while lower back pain was a protective factor. Apart from reporting a significant clinical improvement of patients with CPP associated with dyspareunia after BoNT/A infiltration, this study shows that clinical characteristics should be analyzed in detail to identify potential responders to treatment.