The breeding of the Harpy Eagle now has been studied at several different sites, from Pamama south to Argentina (Fowler and Cope 1964, Rettig 1978, Chebez et al. 1990, De Lucca 1996, Muñiz-Lopez et al. 2007). The nest is in the crown of a tree, usually in a tree that emerges above the canopy; these trees may reach 50-75 m in height. Nests in Guyana and Brazil were placed 33-41 m above the ground (Bond 1927, Fowler and Cope 1964). Five nests in Madre de Dios, Peru ranged in height from 21-27 m, with a mean height of 24.5 m (Piana 2007). The nest site can be lower where the forest has a lower stature; four nests in Misiones, Argentina, were at 16-21 m above the ground, in trees that were only 20-30 m in height (Chebez et al. 1990, De Lucca 1996).
In southeastern Peru, the number of principal branches in an emergent tree is the character most closely associated with nest site selection by Harpy Eagles; emergents with four or more prinicpal branches were the more likely to be used by Harpy Eagles for nesting (Giudice et al. 2007).
Four out of six nests examined in southeastern Peru were in brazil nut trees (Berthollettia excelsa; Lecythidaceae); the two other nests both were in Dipteryx micrantha (Fabaceae) (Piana 2007). Elsewhere the nest often is in a Ceiba (Bierregaard 1994); for example, 8 out of 11 nest trees identified in Ecuador were in Ceiba pentandra (Muñiz-Lopez et al. 2007). Ceiba also has been reported a nest tree in Guyana, as has Mora excelsa (Fowler and Cope 1964). Other tree species reported as nest sites include species of Bombacaceae, Enterolobium contortisiliquum (Fabacese), and Mauritia palms (Bierregaard 1994, De Lucca 1996).
The nest is a large, bulky stick platform; the dimensions of one nest in Guyana were 133 cm across, and 78 cm in height (Rettig 1978). The same nest may be used repeatedly. Rettig (1978), for example, studied a pair in Guyana in 1975 that was at the same site as a pair studied in 1960 by Fowler and Cope (1964). Both sexes contribute to nest construction. The nest primarily is composed of large sticks. These are supplemented with green sprigs; at a nest in Guyana, both sexes brought green sprigs to the nest before egg-laying, but after egg-laying commenced sprigs were provided primarily by the female (Rettig 1978).
The usual clutch size is two, although a clutch of three has been reported. Regardless, in all or almost all cases only a single young is raised, since there are no observations of nests with two large nestlings.
Incubation begins after the second egg is laid, and the incubation period is 56 days (Rettig 1978). Almost all of the incubation is performed by the female, as is the feeding of the hatchiling (Rettig 1978). The male provisions the incubating female periodically. At one nest in Guyana, the male brought prey to the nest about once a week during incubation, and about every 3.5 days during the first half of the nestling period (Rettig 1978). After bringing prey to the nest, the male incubated while the female ate (Rettig 1978). Later in the nestling period, when both adults were hunting, prey was brought to the nest an average of every 2.5 days (Rettig 1978).
At one nest in Guyana (Rettig 1978), the nestling first attempted to stand at 26 days of age. By 36 days, the nestling could stand, and could walk, but only clumsily. Fledging occurs ca four and a half to six months after hatching. Following fledging, the juvenile remains within 100 m of the nest for up to 12 months. During this period the juvenile is dependent upon the adults for food. In a frequently-noted display (Fowler and Cope 1964, Rettig 1978), the dependent juveniles involves calling while flashing the partially-opened wings.
Due to this slow pace of the development of the young, successfully nesting pairs can breed only during every second or third year.