We present a first-principles theoretical approach to calculate temperature dependent phonon dispersions in bcc Fe, which captures finite temperature spin-lattice coupling by treating thermal disorder in both the spin and lattice systems simultaneously. With increasing temperature, thermal atomic displacements are found to induce increasingly large fluctuations in local magnetic moment magnitudes. The calculated phonon dispersions of bcc Fe show excellent agreement with measured data over a wide range of temperatures both above and below the magnetic and structural transition temperatures, suggesting the applicability of the developed approach to other magnetic materials.