Acid Red 27 (AR27) is widely used in paper processing, textiles, foods, cosmetics, beverages and medicines. Effluents containing AR27 are discharged daily into the environment which can adversely affect human and animals as AR27 is classified as an endocrine disruptor. This study describes the application of an aerobic and anaerobic baffled constructed wetland (ABCW) reactor in the removal of AR27 from a solution of synthetic wastewater with 50 mg/L AR27 concentration. The ABCW reactor planted with Phragmites australis was set with intermittent aeration and 1 d hydraulic retention time. This system’s performance was evaluated in terms of COD, NH4+, colour and mineralization of intermediates with and without aeration at different concentrations. Based on the performance and analysis of GCMS, FTIR, HPLC a degradation pathway for AR27 was proposed. The system achieved COD removal of 88%, NH4 + removal of 98%, complete decolourization and mineralization. FTIR analysis showed that provision of intermittent aeration contributed to the removal sulphonic groups and aromatic amines. The performance of the ABCW is attributed to the long pathway travelled by the wastewater which increased contact time of pollutants with microbes and rhizomes; and the synergistic effect of the combination of rhizomes, microbes and supplementary aeration.