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Popcorn is an important crop that is grown for consumption and snacks production in Nigeria however; it has low production and poor yield to meet the demand in the country. This study was conducted to determine the effect of magnetic treatment of irrigation water (MTIW) on the percentage germination (GP), growth rate (GR), popping-quality and yield of popcorn under deficit irrigation. MTIW was produced by passing the water through pipe surrounded with neodymium magnet rated 1.3 Tesla. Popcorn (FRESHTOP variety) was planted in 16 buckets for MTIW and 16 buckets for non-magnetic water (NMW, as control). Four levels of water application as the treatments with 100% water requirements (1.5 liters), 80% (1.2 liters), 60% (0.9 liters) and 50% (0.75 liters) were applied to the popcorn irrigated with MTIW or NMW and monitored for 100 days. The popcorn was thinned to 1 bucket-1 and grown in a garden shed of 5 by 5m and 3m high at the center and 2.5m at the edges. GP of the popcorn at 100%, 80%, 60% and 50% for MW were 75%, 88%, 75%, 63% and for NMW, were 50%, 63%, 50% and 50%, respectively. Mean grain yield after shelled for 100%, 80%%, 60% and 50% with MTIW were 43.43, 50.86, 39.65 and 35.80 g/bucket and corresponding grain yield for NMW were 29.20, 39.43, 37.27 and 28.41 gbucket-1. Water applied at 80% produced the highest yield. MTIW increased the yield of popcorn by 48.73%, 28.88%, 6.39% and 26.01% for 100%, 80%, 60% and 50%, respectively. MTIW is recommended for growing ‘FRESHTOP’ variety popcorn.