Abstract It has been proposed that inner hair cell (IHC) synaptopathy, i.e., loss of synapses between spiral ganglion neurons and IHCs, leads to hidden hearing loss (HHL), i.e., poor performance on challenging hearing tasks despite a normal audiogram. However, this has only been tested in animals after exposure to noise or ototoxic drugs, which can cause deficits beyond synaptopathy. Furthermore, the impact of supernumerary synapses on auditory processing has not been evaluated. Here, we studied mice in which IHC synapse counts were increased or decreased by altering neurotrophin 3 (Ntf3) expression in IHC supporting cells. As we previously showed, postnatal Ntf3 knockdown or overexpression reduces or increases, respectively, IHC synapse density and suprathreshold ABR amplitude, without changing cochlear thresholds. Here, we show that IHC synapse density does not influence the magnitude of the acoustic startle reflex or its prepulse inhibition. In contrast, gap-prepulse inhibition, a behavioral test for auditory temporal processing, was enhanced or reduced according to Ntf3 expression levels. These results indicate that cochlear synaptopathy causes temporal processing deficits, which may be a key contributor to the hearing impairments that define HHL. Furthermore, the improvement in temporal acuity achieved by increasing Ntf3 expression and synapse density suggests a therapeutic strategy for improving hearing in noise for individuals with synaptopathy of various etiologies.