EVAL_PERL needs to be set (or not - I'd advise against putting non-display logic into your templates) in your call to Template->new. e.g.,

my $tt = Template->new(
    INCLUDE_PATH        => 'tpl/',
    TRIM                => 1,
    WRAPPER             => 'wrapper.tt',
    EVAL_PERL           => 1,
);
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Also, you might want to consider changing your question's title... You're doing this with Template::Toolkit, but there's a different (and unrelated) Perl templating module called HTML::Template. I originally read your question expecting to answer that HTML::Template doesn't support Perl in templates at all.