Background: Carpal tunnel syndrome is a neuropathy that affects the median nerve. The aim of this review is to synthesize the evidence and perform a meta-analysis on the effects of iontophoresis in people with carpal tunnel syndrome. Methods: The search was carried out using PubMed, Web of Science, Scopus, CINHAL Complete, Physiotherapy Evidence Database, and SciELO. The methodological quality was evaluated using PEDro. A standardized or mean difference meta-analysis (Hedge’s g) using a random-effects model was calculated. Results: Seven randomized clinical trials using iontophoresis for electrophysiological, pain, and functional outcomes were included. The mean of PEDro was 7/10. No statistical differences were obtained for the median sensory nerve conduction velocity (SMD = −0.89; p = 0.27) or latency (SMD = −0.04; p = 0.81), motor nerve conduction velocity (SMD = −0.04; p = 0.88) or latency (SMD = −0.01; p = 0.78), pain intensity (MD = 0.34; p = 0.59), handgrip strength (MD = −0.97; p = 0.09), or pinch strength (SMD = −2.05; p = 0.06). Iontophoresis only seemed to be superior in sensory amplitude (SMD = 0.53; p = 0.01). Conclusions: Iontophoresis did not obtain an enhanced improvement compared to other interventions, but no clear recommendations could be made due to the limited number of included studies and the heterogeneity found in the assessment and intervention protocols. Further research is needed to draw sound conclusions.