The correlation of discharges between single neurons can provide information about the computations and network properties of neuronal populations during the performance of cognitive tasks. In recent years, dynamic modulation of neuronal correlations by attention has been revealed during the execution of behavioral tasks. Much less is known about the influence of learning and performing a task itself. We therefore sought to quantify the correlated firing of simultaneously recorded pairs of neurons in the prefrontal cortex of naïve monkeys that were only required to fixate, and to examine how this correlation was altered after they had learned to perform a working memory task. We found that the trial-to-trial correlation of discharge rates between pairs of neurons (noise correlation) differed across neurons depending on their responsiveness and selectivity for stimuli, even before training in a working memory task. After monkeys had learned to perform the task, correlated firing decreased overall, although the effects varied according to the functional properties of the neurons. The greatest decreases were observed on comparison of populations of neurons that exhibited elevated firing rates during the trial events and those that had more similar spatial and temporal tuning. Greater decreases in noise correlation were also observed for pairs comprising one fast spiking neuron (putative interneuron) and one regular spiking neuron (putative pyramidal neuron) than pairs comprising regular spiking neurons only. Our results demonstrate that learning and performance of a cognitive task alters the correlation structure of neuronal firing in the prefrontal cortex.