In this paper we present analytical breather solutions of the three-dimensional nonlinear generalized GrossPitaevskii equation. We use an Ansatz to reduce the three-dimensional equation with space-and time-dependent coefficients into an one-dimensional equation with constant coefficients. The key point is to show that both the space-and time-dependent coefficients of the nonlinear equation can contribute to modulate the breather excitations. We briefly discuss the experimental feasibility of the results in Bose-Einstein condensates. [8,9], and semiconductor quantum wells [10], the breather excitations play an important role, directly affecting the electronic, magnetic, optical, vibrational and transport properties of the systems.In the above mentioned studies, one usually considers genuine breathers, i.e., solutions which oscillate in time when the nonlinear equation presents constant coefficients (i.e., without modulation). However, in a more realistic scenario the several parameters that characterize the physical systems may depend on both space and time, leading to breather solutions that can be modulated in space and time. The presence of nonuniform and time-dependent parameters opens interesting perspectives not only from the theoretical point of view, for investigation of nonautonomous nonlinear equations, but also from the experimental point of view, for the study of the physical properties of the systems. In this context, in a recent work we have considered modulation of genuine breather solutions in cigar-shaped Bose-Einstein condensates (BECs) with potential and nonlinearity depending on both space and time, in the one-dimensional (1D) case [11].The study of BECs of dilute gases of weakly interacting bosons, realized for the first time in 1995 on vapors of rubidium [12] and sodium [13], constitutes a very interesting scenario to modulate breathers, since they are well described by a threedimensional (3D) Gross-Pitaevskii (GP) equation arising from a mean-field dynamics [14]. In the BEC context, one finds high experimental flexibility to control nonlinearity via Feshbach resonance, and confinement profile via optical lattices and harmonic and dipole traps [15], and there we can also investigate the effects of dimensionality reduction on the soliton solution.In the case of a strong trapping in two spatial directions, the 3D GP equation reduces to the simpler one-dimensional (1D) form, giving rise to the so-called cigar-shaped configuration. The 1D GP equation is a nonlinear Schrödinger equation, which can also be used to investigate pulse propagation in bulk crystals or optical fibers [16]. In a former work, however, the search for analytical solutions of the 1D GP equation with stationary inhomogeneous coefficients has been implemented via similarity transformation [17]. More recently, however, the case of space-and time-dependent coefficients were considered for the cubic [18], the cubic-quintic [19], the quintic [20], and also the GP equation in higher dimensions [21].The similarity transformation wa...