This study examined how levels of neurotransmitters in the lateral prefrontal cortex (LPFC), a region underlying higherorder cognition, are related to the brain's intrinsic functional organization. Using magnetic resonance spectroscopy (MRS), GABA+ and Glx (glutamate + glutamine) levels in the left dorsal (DLPFC) and left ventral (VLPFC) lateral prefrontal cortex were obtained in a sample of 64 female adults (mean age = 48.5). We measured intrinsic connectivity via resting-state fMRI in three ways: (a) via seed-based connectivity for each of the two spectroscopy voxels; (b) via the spatial configurations of 17 intrinsic networks defined by a well-known template; and (c) via examination of the temporal interrelationships between these intrinsic networks. The results showed that different neurotransmitter indexes (Glx-specific, GABA+-specific, Glx-GABA+ average and Glx-GABA+ ratio) were associated with distinct patterns of intrinsic connectivity. Neurotransmitter levels in the left LPFC are mainly associated with connectivity of right hemisphere prefrontal (e.g., DLPFC) or striatal (e.g., putamen) regions, two areas of the brain connected to LPFC via large white matter tracts. While the directions of these associations were mixed, in most cases, higher Glx levels are related to reduced connectivity. Prefrontal neurotransmitter levels are also associated with the degree of connectivity between non-prefrontal regions. These results suggest robust relationships between the brain's intrinsic functional organization and local neurotransmitters in the LPFC which may be constrained by white matter neuroanatomy.