The desorption of O/CO from graphitic carbon surfaces is investigated using a one-dimensional model describing the adsorbate interactions with the surface phonon bath. The kinetics of desorption are described through the solution of a master equation for the time-dependent population of the adsorbate in an oscillator state, which is modified through thermal fluctuations at the surface. The interaction of the adsorbate with the surface phonons is explicitly captured by using the computed phonon density Of states (PDOS) of the surface. The coupling of the adsorbate with the phonon bath results in the transition of the adsorbate up and down a vibrational ladder. The adsorbate-surface interaction is represented in the model using a Morse potential, which allows for the desorption process to be directly modeled as a transition from bound to free (continuum) state. The PDOS is a property of the material and the lattice; and is highly sensitive to the presence of defects. The effect of etch pits along with random surface defects on the PDOS is considered in the present work. The presence of defects causes a redshift and broadening of the PDOS, which in turn changes the phonon frequency modes available for adsorbate coupling at the surface. Using the realistic PDOS distributions, the phonon-induced desorption (PID) model was used to compute the transition and desorption rates for both pristine and defective systems. Mathissen’s rule is used to compute the phonon relaxation time for pristine and defective systems based on the phonon scattering times for each of the different scattering processes. First, the desorption rates of the pristine system is fitted against the experimental values to obtain the Morse potential parameters for each of the observed adatoms. These Morse potential parameters are used along with the defective PDOS and phonon relaxation time to compute the desorption rates for the defective system. The defective system rates (both transition and desorption) were consistently lower in comparison with the pristine system. The difference between the transition rates is more significant at lower initial states due to higher energy spacing between the levels. In the case of the desorption rates, the difference between the defective and pristine system is more significant at higher temperatures. The desorption rates for each of the system shows an order of magnitude decrease with the strongly bound systems exhibiting the greatest reduction in the desorption rates.