Chronic pelvic pain (CPP) is a highly disabling disorder in women usually associated with hypertonic dysfunction of the pelvic floor musculature (PFM). The literature on the subject is not conclusive about the diagnostic potential of surface electromyography (sEMG), which could be due to poor signal characterization. In this study, we characterized the PFM activity of three groups of 24 subjects each: CPP patients with deep dyspareunia associated with a myofascial syndrome (CPP group), healthy women over 35 and/or parous (>35/P group, i.e., CPP counterparts) and under 35 and nulliparous (<35&NP). sEMG signals of the right and left PFM were recorded during contractions and relaxations. The signals were characterized by their root mean square (RMS), median frequency (MDF), Dimitrov index (DI), sample entropy (SampEn), and cross-correlation (CC). The PFM activity showed a higher power (>RMS), a predominance of low-frequency components (<MDF, >DI), greater complexity (>SampEn) and lower synchronization on the same side (<CC) in CPP patients, with more significant differences in the >35/P group. The same trend in differences was found between healthy women (<35&NP vs. >35/P) associated with aging and parity. These results show that sEMG can reveal alterations in PFM electrophysiology and provide clinicians with objective information for CPP diagnosis.