In the present work, the chemical regulation of intracellular kinase activity has been studied by a peptide microarray-based resonance light scattering (RLS) assay with gold nanoparticle (AuNP) probes. After interactions of five cell lines and seven compounds (six potential inhibitors of cyclic adenosine monophosphate (cAMP)-dependent protein kinase A (PKA) and Forskolin (Fsk)), we found that the intracellular PKA activity is strongly regulated by the extracellular compounds and that the compounds affect the intracellular PKA activity in a dose-dependent manner. The experimental results demonstrate that the peptide microarray-based RLS assay can be employed to quantitatively determine the efficiency of the inhibitor/activator on the kinase activity at the cellular level. In addition, chemical-mediated fluctuation of the PKA activity in different cell phases (e.g., G2/M phase and M/G1 phase) was successfully detected, which also demonstrates the utility of the approach for monitoring chemical regulation of intracellular kinase activity.