use strict;
use warnings;

my $source = <<STR;
I have a file with 50,000 lines of find and replace string.
For example
/Test/Sample/
/A/X/
Now i want to process the file with input file.
I have tried with usual method, it takes more than 1 hour.
Please advice.
STR

my $matches = <<STR;
/advice/advise/
/usual/the usual/
/lines/wobbles/
/file/flibble/
STR

my %replace;

open my $repIn, '<', \$matches;
while (<$repIn>) {
    next if ! m{/([^/]+)/([^/]+)/};
    $replace{lc $1} = $2;
}
close $repIn;

my $match = join '|', keys %replace;

open my $srcIn, '<', \$source;
while (<$srcIn>) {
    s/($match)/$replace{lc $1}/eig;
    print;
}