Radiofrequency equipment, including invasive fractional microneedle radiofrequency (FMR) and noninvasive fractional radiofrequency (FR), has facilitated progress in the field of active acne treatment, but clinical data are limited. This study aimed to compare the efficacy and safety of FMR and FR in the treatment of moderate-to-severe acne vulgaris. Ten patients with moderate-to-severe acne were enrolled in a 24-week, prospective, single-blind, randomized, comparative clinical trial with a split-face design. Fractional microneedle radiofrequency treatment was provided on one side of the face and FR on the opposite side. Three consecutive treatments were performed at 4-week interval. Objective assessment of efficacy was performed using the Acne Severity Index (ASI), and acne inflammatory lesions and noninflammatory lesions were evaluated. After the first treatment, ASI and both inflammatory and noninflammatory lesions of the FMR-treated side were improved to a greater degree than the FR-treated side. Patients' subjective satisfaction was also better regarding the FMR-treated side. After subsequent treatments, efficacy improves for both groups, and no significant differences in the above efficacy parameters between the two groups were observed. Pain scores were significantly higher for the FR-treated side than the FMR-treated side. Fractional microneedle radiofrequency is faster and more effective than FR for the treatment of moderate and severe acne after only one treatment. However, after several treatment sessions, both FMR and FR proved to be safe and effective for long-term treatment of moderate-to-severe acne. Therefore, invasive radiofrequency, such as FMR, or noninvasive radiofrequency, such as FR, can successfully treat active acne.