Simulink Profiler adds some overheads in the background to the functions or models being profiled. Since it gives the detailed execution time for each function during simulation, it is the best way to judge the performance of just the "simulation phase".
However, if you do not want to recompile your Simulink model, say for different iterations, consider using the "Fast Restart" option with "tic-toc". Find more information about the "Fast Restart" option in the following link:
Consider the simulation of the model "vdp" with a MATLAB script:
for i=1:4
tic
sim('vdp','FastRestart','on');
toc
end
The first run of the model involves compilation, but not the three subsequent ones. The timing adheres more to the "simulation phase" in the last three simulations.
