There're free and paid tools for encode your php script. Personally I like Byterun Online Free PHP Encoder for a small job, it's an online tool and cost nothing but if you're in a big project you may looking for other tools.

What will happenned to PHP scripts after encoded

Example
Before encode
<?php
echo "Hello World";
?>

After encoded
<?php $_F=__FILE__;$_X='Pz48P3BocA0KNWNoMiAiSDVsbDIgVzJybGQiOw0KPz4=';
eval(base64_decode('JF9YPWJhc2U2NF9kZWNvZGUoJF9YKTskX1g9c3RydHIoJF9YLC
cxMjM0NTZhb3VpZScsJ2FvdWllMTIzNDU2Jyk7JF9SPWVyZWdfcmVwbGFjZSgnX19GS
UxFX18nLCInIi4kX0YuIiciLCRfWCk7ZXZhbCgkX1IpOyRfUj0wOyRfWD0wOw=='));?>

As you see PHP code after encoded, you don't understand it, but this code still executable and the result is the same as result before encode.

Here is the list of tools