Aluminum (Al) alloy 6061 is often used in engineering applications due to its high strength, excellent fracture toughness, and corrosion resistance. Lots of material removal or machining processes would induce some undesirable side effects like surface damages, fractures, and erosions. In this study, the surface defects in the workpieces caused by the electrical discharge machining process were eliminated with the plasma etching treatment. Meanwhile, the surface integrity and the fatigue properties of the workpiece improved significantly. Surface roughness, contact angle, and morphology were investigated by varying plasma etching parameters such as the etching power, oxygen gas flow, and the etching time. Furthermore, the optimum process conditions were evaluated using statistical analyses. The workpiece treated with the plasma etching had the smallest roughness of 12.2 mm, the largest contact angle of 92°, and 25% increase in the fatigue life. These experimental results indicated that the surface characteristics of the workpiece had a great influence on the fatigue life of electrical discharge machined Al alloy.