Continuous and intermittent microwave-assisted extractions were used to extract pectin from banana peels. Extraction parameters which were employed in the continuous process were microwave power (300–900 W), time (100–300 s), pH (1–3) and in the intermittent process were microwave power (300–900 W), pulse ratio (0.5–1), pH (1–3). The independent factors were optimized with the Box–Behnken response surface design (BBD) (three factor three level) with the desirability function methodology. Results indicate that the independent factors have substantial effect on the pectin yield. Optimized solutions for highest pectin yield (2.18%) from banana peels were obtained with microwave power of 900 W, time 100 s and pH 3.00 in the continuous method while the intermittent process yielded the highest pectin content (2.58%) at microwave power of 900 W, pulse ratio of 0.5 and pH of 3.00. The optimized conditions were validated and close agreement was observed with the validation experiment and predicted value.