To add to this - I usually use the full path or a relative path (I hate modifying the PATH). I find that FindBin and File::Spec are incredibly useful for this.

use FindBin;
use File::Spec;
use lib File::Spec->catdir($FindBin::Bin, 'lib'); # get modules from t
+he lib subdirectory under this perl script

#...

my $exe = File::Spec->catfile($FindBin::Bin,
   File::Spec->updir(),
   qw(PDFtoHTML pdftohtml));
system($exe, $pdffile) == 0 or do {
  # handle system error.
}
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