An alternative discretization and solution procedure for implicitly solving a 3-D microscale heat transport equation during femtosecond laser heating of nanoscale metal films has been developed (Kunadian et al. [1]). The proposed numerical technique directly solves a single partial differential equation, unlike other techniques available in the literature which splits the equation into a system of two equations and then apply discretization. The present paper investigates performance of its split and unsplit methods of solution via numerical experiments using Gauss–Seidel, conjugate gradient, generalized minimal residual and δ-form Douglas–Gunn time-splitting methods to compare the computational cost involved in these methods. The comparison suggests that the unsplit method [1] employing δ-form Douglas–Gunn spatial time-splitting is the most efficient way in terms of CPU time taken to complete the simulation of solving the 3-D time dependent microscale heat transport equation.