Ok, I can see why that would be slow. Without knowing more about the nature of the find and replace strings it's hard to suggest any specific solution that are guaranteed to help, but the following technique may help:

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;
}
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Prints:

I have a flibble with 50,000 wobbles of find and replace string.
For example
/Test/Sample/
/A/X/
Now i want to process the flibble with input flibble.
I have tried with the usual method, it takes more than 1 hour.
Please advise.
[download]