Purpose: The objectives of this study were to determine the enhancing effect of iontophoresis method as it transdermally deliver methylene blue (MB) using visual examination, in terms of penetration depth and tissue distribution in the skin, and to determine the effect of application duration on the efficacy of iontophoresis. Methods: Twenty-four male Sprague-Dawley rats were randomly divided into 5-, 10-, 20-, and 40-minute groups. These rats were exposed to either topical or anodic iontophoresis of 1% MB using a direct current of $0.5mA/cm^2$ for 5, 10, 20, and 40 minutes. Using cryosections of rat tissues, the penetration depth of MB was measured using light microscopy. Results: Significant differences in the penetration depth (F=54.20, p<0.001) were detected among the four groups. Post hoc comparisons of the penetration depth of MB data pooled across groups showed no significant difference between all topical application groups and 5-minute iontophoresis group, but did reveal a significant difference in the penetration depth between all topical application groups and 5-minute iontophoresis group versus 10-minute group, between the 10-minute and 20-minute group, and between the 20-minute and 40-minute iontophoresis group (p<0.05). Conclusion: The results demonstrate that iontophoresis enhances transdermal delivery of MB across stratum corneum of skin barrier by visual examination. Furthermore, the penetration depth of iontophoretic transdermal delivery of MB was dependent on the application duration. The duration of iontophoresis is one of the important factor in the efficacy of iontophoresis application.