The prefrontal cortex (PFC) has been postulated to play critical roles in cognitive control and the formation of long-term memories. To gain insights into the neurobiological mechanism of such high-order cognitive functions, it is important to understand the input-output transformational properties of the PFC micro-circuitry. In this study, we identify the functional connectivity between the Layer 2/3 (input) neurons and the Layer 5 (output) neurons using a previously developed generalized Volterra model (GVM). Input-output spike trains are recorded from the PFCs of nonhuman primates performing a memory-dependent delayed match-to-sample task with a customized conformal ceramic multi-electrode array. The GVM describes how the input spike trains are transformed into the output spike trains by the PFC micro-circuitry and represents the transformation in the form of Volterra kernels. Results show that Layer 2/3 neurons have strong and transient facilitatory effects on the firings of Layer 5 neurons. The magnitude and temporal range of the input-output nonlinear dynamics are strikingly different from those of the hippocampal CA3-CA1. This form of functional connectivity may have important implications to understanding the computational principle of the PFC.