The present study comprehensively compared the microstructure, flexural strength, and fracture toughness of zirconia ceramics prepared via two different methods, subtractive milling (SM) and stereolithography (SLA). Disc- or rectangular-shaped zirconia specimens (Prettau (SM) and 3DMix Zirconia (SLA)) were prepared following each manufacturer’s instructions and polished. The microstructures of the two different zirconia specimens were studied by scanning electron microscopy, X-ray diffractometry, energy-dispersive X-ray spectroscopy, and electron backscattered diffractometry. The flexural strength and fracture toughness based on the indentation fracture method were measured for the two different zirconia ceramics. A greater number of small pores and smaller grains were found in the SLA specimen than in the SM specimen. The crystal structure and microstructure analysis revealed that both ceramics had a similar phase composition to each other. No significant differences in flexural strength (p = 0.242) or fracture toughness (p = 0.101) were detected between the two ceramics. The mean flexural strength of the SLA-fabricated zirconia as well as the SM zirconia satisfied the class 5 criteria (>800 MPa) in the ISO 6872 standard.