Infrared multiple photon dissociation (IRMPD) kinetics measured with tunable laser radiation from a free electron laser (FEL) are used to probe the relative populations of and interconversions between energetically competitive isomers of gas-phase ions at 298 K. On-resonance IRMPD kinetics of monoisomeric benzoate anion and anilinium (protonated aniline) are measured to determine the extent of overlap of the laser beam with the precursor ion population (∼93%). IRMPD kinetics indicating different photodissociation behavior for different isomers obtained at isomer-specific resonances are used to determine relative populations of salt bridge and charge-solvated isomers for ArgGly·Na(+), Ser·Cs(+), and Arg·Na(+). These values and Gibbs free energy differences obtained from them for thermal precursor populations are compared to values reported using other, less direct population probes. Rapid interconversion of two charge-solvated isomers occurs for ArgGly·Li(+), precluding population analysis for this ion. ArgGly·Na(+), ArgGly·Li(+), and Arg·Na(+) exhibit IRMPD induction periods lasting many seconds for some isomers at the laser photon energies and power used, indicating that IRMPD relative spectral intensities are time-dependent for these ions and that the relative band intensities in IRMPD spectra measured with short irradiation times may not provide meaningful information about relative isomer populations. These results constitute the first direct probe of ion isomer populations using IRMPD kinetics obtained with a FEL and illustrate a number of caveats in interpreting IRMPD spectra measured with just a single irradiation time. These results also indicate that more complete overlap of the laser beam with the ions will be highly advantageous in future instrument designs for IRMPD kinetics and spectroscopy experiments.