Our study compared treatment efficacy between cut-off and notch filters in intense pulsed light (IPL) therapy for meibomian gland dysfunction (MGD) through a prospective, randomized paired-eye trial. Additionally, the efficacy of IPL treatment alone was investigated by restricting other conventional treatments. One eye was randomly selected for an acne filter and the other for a 590-nm filter. Identical four regimens of IPL treatments were administered. The tear break-up time (TBUT), Oxford scale, Sjögren’s International Clinical Collaborative Alliance (SICCA) staining score, tear matrix metalloproteinase-9 (MMP-9) expression, tear osmolarity, and Ocular Surface Disease Index (OSDI) questionnaires were evaluated before and after IPL. Meibomian gland (MG) parameters were measured. When combining the results from both filters, the TBUT, SICCA staining score, OSDI score, and upper and lower lid meibum expressibility were improved after IPL. No significant differences were found between the two filters in the TBUT, Oxford scale, SICCA staining score, MMP-9 expression, tear osmolarity, and MG parameters. Although not significant, the acne filter showed better treatment efficacy than that in the 590-nm filter. IPL alone is efficacious in terms of ocular surface parameters, MG function, and subjective symptoms. Regarding filter selection, both acne and 590-nm filters are promising options for MGD treatment.