Fatigue tests of friction stir welded (FSWed) joints of A6061-T6 aluminum alloy have been conducted with fully reversed plane bending conditions (R= -1) to investigate the effect of shot peening on the high cycle fatigue property. Shot peening was performed with two types of fine zirconia shot grid. The results showed that the fatigue strength at 10⁷ cycles of unwelded specimens (base material) was 130 MPa and fine zirconia shot peening enhanced the strength by 10 MPa with B120 shot grid type. The fatigue lives were dramatically improved in all stress levels by the peening. On the other hand, the fatigue strength at 10⁷ cycles of the SP treated FSWed specimens was nearly the same as that of the base material, and the fatigue lives were improved at only lower stress levels. To discuss these fatigue properties, fracture surfaces were observed and peening effects such as surface roughness, hardness and residual stress distributions were examined.