MCBTE solves the linearized Boltzmann transport equation for phonons in three-dimensions using a variance-reduced Monte Carlo solution approach. The algorithm is suited for both transient and steady-state analysis of thermal transport in structured materials with size features in the nanometer to hundreds of microns range. The code is portable and integrated with both first-principles density functional theory calculations and empirical relations for the input of phonon frequency, group velocity, and mean free path required for calculating the thermal properties. The program outputs space- and time-resolved temperature and heat flux for the transient study. For the steady-state simulations, the frequency-resolved contribution of phonons to temperature and heat flux is written to the output files, thus allowing the study of cumulative thermal conductivity as a function of phonon frequency or mean free path. We provide several illustrative examples, including ballistic and quasi-ballistic thermal transport, the thermal conductivity of thin films and periodic nanostructures, to demonstrate the functionality and to benchmark our code against available theoretical/analytical/computational results from the literature. Moreover, we parallelize the code using the Matlab Distributed Computing Server, providing near-linear scaling with the number of processors. Program summaryProgram Title:MCBTECPC Library link to program files:https://doi.org/10.17632/rzn86w7t3p.1Developer's repository link:https://github.com/abhipath90/MCBTECode Ocean capsule:https://codeocean.com/capsule/7196257Licensing provisions: GPLv3Programming language: MATLABNature of problem: Calculation of time- and space-dependent temperature and heat flux profiles, and frequency-resolved effective thermal conductivity in structured systems where heat is carried by phonons.Solution method: Solution of linearized Boltzmann transport equation for phonons, variance-reduced Monte Carlo approach.Additional comments including restrictions and unusual features: Runtime about 1 to 10 hours on a personal computer.