One of the most important challenges in developing the concrete industry is to use sustainable materials that are able to improve concrete properties. Magnetized water (MW) is a type of water that can replace tap water (TW) in conventional concrete and enhance its mechanical properties. However, the performance of MW in geopolymer concrete has not been well investigated up to now. The goal of this study is to measure the effect of using an alkaline activator (AA) made of MW on the mechanical properties and durability of fly ash (FA)-based geopolymer concrete. The AA was a mixture of sodium hydroxide (SH) solution and sodium silicate (SS) solution. Eighteen geopolymer concrete mixes were tested for several fresh, hardened, and durability properties. Of these mixes, nine were prepared with AA made of MW and the other nine were the same but prepared with AA made of TW. The preparation of MW was simply carried out by passing TW across permanent magnets of 1.6 Tesla, and then 1.4 Tesla intensities for 150 cycles. The MW-based AA properties were analyzed and compared to those of the conventional TW-based AA. Several mechanical and durability properties were measured. Scanning electronic microscopy (SEM) analysis was also conducted on selected mixes. The outcomes of the hardened concrete tests demonstrated that while using MW to prepare AA solution contained SH with a molarity of 16 M, an SS/SH ratio of 2, an AA/C ratio of 0.4, a W/C ratio of 10%, and a curing temperature of 115 °C could display the best outcomes in this study when used in geopolymer concrete. Using MW in a geopolymer concrete AA could increase its slump by up to 100% compared to that made of TW. Using MW in the AA enhanced the compressive strength by up to 193%, 192%, and 124% after 7, 28, and 56 days, respectively. The SEM analysis showed that using MW clearly enhanced the surface morphology of geopolymer concrete. The proposed geopolymer concrete made using the MW-based AA in this study sheds the light on a new class of eco-friendly concrete that could possibly be used in many structural applications.