Al-Si-Mg 4xxx filler metals are widely used in aluminum welding owing to their excellent weldability and capability for strength enhancement by heat treatment. However, weld joints with commercial Al-Si ER4043 fillers often exhibit poor strength and fatigue properties. In this study, two novel fillers were designed and prepared by increasing the Mg content in 4xxx filler metals, and the effects of Mg on the mechanical and fatigue properties were studied under as-welded and post-weld heat-treated (PWHT) conditions. AA6061-T6 sheets were used as the base metal and welded by gas metal arc welding. The welding defects were analyzed using X-ray radiography and optical microscopy, and the precipitates in the fusion zones were studied using transmission electron microscopy. The mechanical properties were evaluated using the microhardness, tensile, and fatigue tests. Compared to the reference ER4043 filler, the fillers with increased Mg content produced weld joints with higher microhardness and tensile strength. Joints made with fillers with high Mg contents (0.6–1.4 wt.%) displayed higher fatigue strengths and longer fatigue lives than joints made with the reference filler in both the as-welded and PWHT states. Of the joints studied, joints with the 1.4 wt.% Mg filler exhibited the highest fatigue strength and best fatigue life. The improved mechanical strength and fatigue properties of the aluminum joints were attributed to the enhanced solid-solution strengthening by solute Mg in the as-welded condition and the increased precipitation strengthening by β″ precipitates in the PWHT condition.