The mock that I created is a very simple C program that would need to be compiled before running the tests using a Makefile already available.

There might be an easier way... but if all else fails, you can always add an extra target (which builds you C program) to the generated Makefile and add it as a prerequisite to the test target, so that your program would be built right before testing.

Something like this (assuming you have your C stuff in a subdirectory mymock, and that mymock/Makefile would build the target executable mymock/mymock):

### Makefile.PL

WriteMakefile(
    ...
);

package MY;

# override / modify test target
sub test {
    my $t = shift->SUPER::test(@_);
    $t =~ s|^test ::\K| mymock/mymock |m;  # inserts your prereq
    return $t;
}

# add your own target
sub postamble {
    return <<'MAKE_MOCK';
mymock/mymock : mymock/Makefile
    cd mymock && $(MAKE) all

MAKE_MOCK
}
[download]

(untested)

See also Overriding MakeMaker Methods.

Portability might well be an issue here, so you might ultimately be better off implementing your mock program in pure Perl... (if that's possible)