system('/bin/ksh', '-c', '. /env.ksh ; shellFunction');

##</code><code>##

my $pid = open my $shell, "| /bin/ksh" or die "Couldn't start ksh: $!";
print $shell ". /env.ksh\n";

print $shell "shellFunction\n";

# later
print $shell "shellFunction2\n";
# ...