Annatto (Bixa orellana L.), a tropical plant, has a promising place in industrial sector notably in food sector due to increasing consumer demand for complete natural products. The pigments obtained from the seed coat of annatto have the property of imparting colours ranging from red to yellow, and these colours are used as a natural colourant in foods. The major colouring pigments present are bixin and norbixin. Modern extraction methods are required to improve the yield of pigments with less energy consumption. The present work focuses on microwave assisted aqueous extraction of pigments from annatto seeds by varying the seed to water ratio (1:1, 1:2, and 1:3 w/v), temperature (50, 60, and 70 °C), and extraction time (10, 20, and 30 min) at 700 W and it was compared with hot aqueous extraction using Box-Behnken design. The treatment combination during hot aqueous and microwave-assisted extraction having seed to water ratio, temperature, and residence time of 1:1, 50 °C, and 30 min and 1:1, 70 °C, and 30 min showed better yield of 0.237% and 0.625% bixin, and 2.31% and 3.008% of norbixin, respectively. The optimized extraction conditions performed at seed to water ratio of 1:1 at 60 °C for 30 min using microwave-assisted extraction was recommended to provide the maximum yield of bixin and norbixin pigments.