The perl_parse() function probably does what you're looking for. From perlapi:

perl_parse
   Tells a Perl interpreter to parse a Perl script.
   See perlembed.
      int perl_parse(
         PerlInterpreter* interp,
         XSINIT_t xsinit,
         int argc,
         char** argv,
         char** env)
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perlembed has some examples using; the argv parameter in perl_parse(). Another bare one could be something like this (vaguely inspired by the PerlPower example but omitting all the surrounding stuff):

#include <EXTERN.h>
#include <perl.h>

static PerlInterpreter *my_perl;

int main (int argc, char *argv[], char *env[]) {
   char *private_argv[] = { "", "script.pl", "some", "args" };
   my_perl = perl_alloc();
   perl_construct(my_perl);
   perl_parse(my_perl, NULL, 4, private_argv, NULL);
   perl_run(my_perl);
   /* ... */
}
/* ... */
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Note that these are arguments as you would find in a real command line; this means that -e, for example, gets caught by the perl_parse() function, which looks for the next argument to find an inline sequence of statements. There are a couple of examples in perlembed that use this feature.