PHP gets compiled to bytecode on the server before being executed.
You can cache the pre-compiled code with (for example) APC.
Unless your code is several thousand lines of code (or your server
very slow... 486-slow), the compilation phase is not that long.
I think your main problem can be one of:
1- wrong algorithm
2- long waits (database, files, network, etc.)
3- heavy calculations
1- find and use a different algorithm
2- Try to parallelize code (with gearman or similar, or via
3- rewrite the heavy functions in C, C++ or Go and compile them, then
call them via PHP extensions or via gearman/fork.