In many species of birds, periods of incubation of eggs within a clutch depend on the order in which the eggs were laid and determine whether the eggs hatch asynchronously or on the same day. Magellanic Penguins (Spheniscus magellanicus) lay two eggs 4 days apart that hatch 2 days apart; first eggs take 41 days to hatch, and second eggs take 39 days. We tested whether temperatures of the two eggs differ and whether delayed onset of incubation caused this pattern. First eggs were cooler than second eggs during their first few days (P < 0.001). First eggs averaged 23.4 ± 0.3 °C in the first 24–48 hours after they were laid. Second eggs averaged 27.9 ± 0.3 °C, warm enough for development. Egg temperature did not stabilize (33.9 °C) until eggs were about 18 days old. We swapped first and second eggs of different nests to determine if parental behavior caused the differences in temperatures and incubation periods. First eggs treated as second eggs developed as fast as control second eggs, and second eggs treated as first eggs developed nearly as slowly (40 days) as control first eggs. First eggs that were stored in a cooler until second eggs were laid took 2 days longer to hatch than control first eggs. Parental incubation behavior explained why the incubation period of second eggs was shorter than that of first eggs and controlled asynchrony of hatching, which affects chick growth and survival.