Instead of substitution or matching you could use tr.

$ perl -Mstrict -Mwarnings -E '
open my $fastaFH, q{<}, \ <<EOF or die $!;
> Seq 1
CTGTCA
GTCCTC
> Seq 2
GGCTA
> Seq 3
CATGAG
ATTCG
EOF

my $seqCt = 0;

$seqCt += tr{>}{} while <$fastaFH>;

say $seqCt;'
3
$
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I hope this is of interest.