You're not stupid, after all you answered your own question correctly. The '?' in the first $b is indeed being interpreted as a metacharacter. To prevent this, use the \Q...\E codes in your regular expression (or the quotemeta builtin outside it): 

$a = "http://www.myurl.com/e.php?a";
$b = "http://www.myurl.com/e.php?a";
if ($a =~ /\Q$b\E/) {       # <---------
        print "FOUND\n";
} else {
        print "NOT FOUND\n";
}

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In reply to Re: Regular expression help: why does this not match? by gaal
in thread Regular expression help: why does this not match? by lokiloki

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