Post-stroke flexion synergy limits arm/hand function and is also linked to hyperactive stretch reflexes or spasticity. It is implicated in the increased role of indirect motor pathways following damage to direct corticospinal projections. We hypothesized that this maladaptive neuroplasticity also affects stretch reflexes. Specifically, multi-synaptic interactions in indirect motor pathways may increase nonlinear neural connectivity and time lag between stretch and reflex muscle response. Continuous position perturbations were applied to the elbow joint when eleven participants with stroke generated two levels of shoulder abduction (SABD) torques with their paretic arm to induce synergy-related spasticity. Likewise, the perturbations were applied to eleven control subjects while performing SABD and elbow flexion levels matching the synergy torques in stroke. We quantified linear and non-linear connectivity and the corresponding time lags between perturbations and muscle activity. Enhanced nonlinear connectivity with a prolonged time lag was found in stroke as compared to controls. Non-linear connectivity and time lag also increased with the expression of the flexion synergy, as induced by greater SABD load levels, in stroke. This study provides new evidence of changes in neural connectivity and long-latency time lag in the stretch reflex response post-stroke. The results suggest the contribution of indirect motor pathways to synergy-related spasticity.