This work develops a Monte Carlo (MC) simulation method for calculating the heat generation rate in electronic nanostructures. Electrons accelerated by the electric field scatter strongly with optical phonons, yet heat transport in silicon occurs via the faster acoustic modes. The MC method incorporates the appropriate energy transfer rates from electrons to each phonon branch. This accounts for the non-equilibrium energy exchange between the electrons and phonon branches. Using the MC method with an electron energy-dependent scattering rate intrinsically accounts for the non-locality of the heat transfer near a strongly peaked electric field. This approach provides more information about electronically generated heat at nanoscale dimensions compared to traditional macroscopic field-dependent methods. The method has applications in any region of high spatial or temporal non-equilibrium between electrons and phonons, and particularly facilitates careful microscopic analysis of heating in a nanoscale transistor.