Ok, that sounds very doable. One of the best things about Comsol is that pretty much everything can depend on nearly everything and it gives the user lots of tools to solve complex problems.
For example one can define a boundary condition, say for an edge, as a function of time by simply writing the boundary condition as a function of time to the appropriate cell, when have opened the "boundary condition" window. So you can define all sorts of dependencies straight to the respective "cells" in the GUI (like if you take a look at boundary settings in a heat transfer problem you'll see a selection of boundary condition options [heat flux, temperature, isolation etc.] which you can then define as you like) as a function of whatever you want (pretty much the only limitation being that the problem remains solvable and everything is 'defined') using the matlab-like notation of Comsol.
For example, if I'd want to define a linear boundary condition as a function of time, I'd just specify a+b*t (a,b constants, t in comsol is reserved for time) for that boundary in question for what quantity I'm interested in specifying.
So I'd think the next question is how well is your boundary condition defined at the moment, do you have it already written down well enough that it would "just" be about inputting it or does it require an additional solution of some sort or coupling to the solution of the thermal problem (like do you have a known pressure variation with time etc. which could be used to define it)?