Since Pixley Refuge consists primarily of the Valley Grassland plant community, many grassland bird species nest on the Refuge these species include: Horned Lark, Western Meadowlark, and various species of sparrow. Wet marshes provide habitat for migrating and wintering birds. Sandhill Cranes are the most prominent species that roost on Pixley Refuge wetlands. Cranes begin arriving from northern nesting grounds in September and numbers may peak at around 6,000 birds by January. At times, up to 600 Canada Geese have been observed feeding in the grasslands.
Some species of waterfowl seen on the moist soil units in the winter are Northern Shovelers, Gadwalls, Mallards, American Wigeons, and Northern Pintails. These same areas also provide wintering habitat for White-faced Ibis. In recent years on a single day, more than 2,000 ibis have been counted roosting in the wetlands. Wintering and migrating shorebirds also use the Refuge and include Black-necked Stilts, Greater Yellowlegs, American Avocets, and Killdeer. Wading birds also frequent Pixley Refuge and may include Black-crowned Night Heron, Cattle Egret, American Bitterns, and Great-blue Herons.
Some birds of prey common to Pixley Refuge include Red-tailed Hawks, American Kestrel, Burrowing Owl, and Black-shouldered Kites.