Aims: Small fiber neuropathy/polyneuropathy (SFN) has been found to be present in 64% of complex (refractory or multisystem) chronic pelvic pain (CPP) patients. The small fiber dysfunction seen in SFN can negatively impact autonomic control of micturition in addition to pain. This study investigated the clinical association of autonomic dysfunction (detrusor underactivity and primary bladder neck obstruction [BNO]) on video urodynamics (VUDS) with SFN in patients with CPP.Methods: This was a retrospective observational study, querying data from patients with complex CPP. Inclusion criteria were: the presence of complex (refractory or multisystem) CPP, and completion of both (1) subspecialty autonomic neurology evaluation for SFN and (2) high-quality VUDS performed according to ICS standards. Autonomic bladder dysfunction (BNO or detrusor underactivity) on VUDS was compared to the presence of SFN.Results: Thirty-two female patients with complex CPP met criteria. Of the 32, 23 (72%) were found to have SFN. Patient with autonomic bladder dysfunction (BNO or detrusor underactivity) were more likely to have SFN (OR = 9.5 [95% CI: 1.641, 55.00], p = 0.007). Post-void residual volume was higher in the SFN group (p = 0.011 [95% CI: 13.12, 94.0]) and symptoms of urge urinary incontinence were more likely to be present (p = 0.000 [95% CI: −3.4, −1.25]).Conclusions: Patients with complex CPP with autonomic bladder dysfunction are more likely to have SFN. This suggests patients with complex CPP should be considered for diagnosis and treatment of SFN, particularly if BNO or detrusor underactivity is noted on VUDS evaluation.