A result of great theoretical and experimental interest, the Jarzynski equality predicts a free energy change ΔF of a system at inverse temperature β from an ensemble average of nonequilibrium exponential work, i.e., 〈e^{-βW}〉=e^{-βΔF}. The number of experimental work values needed to reach a given accuracy of ΔF is determined by the variance of e^{-βW}, denoted var(e^{-βW}). We discover in this work that var(e^{-βW}) in both harmonic and anharmonic Hamiltonian systems can systematically diverge in nonadiabatic work protocols, even when the adiabatic protocols do not suffer from such divergence. This divergence may be regarded as a type of dynamically induced phase transition in work fluctuations. For a quantum harmonic oscillator with time-dependent trapping frequency as a working example, any nonadiabatic work protocol is found to yield a diverging var(e^{-βW}) at sufficiently low temperatures, markedly different from the classical behavior. The divergence of var(e^{-βW}) indicates the too-far-from-equilibrium nature of a nonadiabatic work protocol and makes it compulsory to apply designed control fields to suppress the quantum work fluctuations in order to test the Jarzynski equality.