I have created a config to put in your .ebextensions folder. I was not able to find a single tutorial or blog post showing you how to get Phalcon working on EB so here it is:

# Lets install all the packages its needs
# Source: http://phalconphp.com/en/download
    php55-devel.x86_64: []
    gcc.noarch: []
    libtool.x86_64: []
    git.x86_64: []

  # Lets makes sure we're working with a clean directory
    command: "rm -rf cphalcon"
    cwd: /tmp

  # Clone the repo
    command: "git clone --depth=1 git://github.com/phalcon/cphalcon.git"
    cwd: /tmp

  # Compile and install it
    command: "./install"
    cwd: /tmp/cphalcon/build

  # Put the extension into an ini file so PHP can find it.
command: "echo 'extension=phalcon.so' > /etc/php-5.5.d/phalcon.ini"

Thats it! Put this file in your .ebextensions folder with a name something like 02phalcon.config and you should be good to go.

One thing to note is that it references a very specific version of php aka /etc/php-5.5.d. So when you deploy if you're changing the PHP version that part will need to be updated.

This tip refer at https://devtheops.com/installing-phalcon-php-on-elastic-beanstalk-a53b331c623e