If you want to add custom.js script that is located in the js/ folder of your theme, you'll need to enqueue it. In functions.php add

<?php

add_action( 'after_setup_theme', 'yourtheme_theme_setup' );

if ( ! function_exists( 'yourtheme_theme_setup' ) ) {
    function yourtheme_theme_setup() {

        add_action( 'wp_enqueue_scripts', 'yourtheme_scripts' );
        add_action( 'admin_enqueue_scripts', 'yourtheme_admin_scripts' );

    }
}

if ( ! function_exists( 'yourtheme_scripts' ) ) {
    function yourtheme_scripts() {

        wp_enqueue_script( 'yourtheme_custom', get_template_directory_uri().'/js/custom.js', array( 'jquery' ), '1.0.0', true );

    }
}

if ( ! function_exists( 'yourtheme_admin_scripts' ) ) {
    function yourtheme_admin_scripts() {

        wp_enqueue_script( 'yourtheme_custom', get_template_directory_uri().'/js/custom.js', array( 'jquery-ui-autocomplete', 'jquery' ), '1.0.0', true );

    }
}

add_action( 'wp_enqueue_scripts', 'enqueue_my_styles_and_scripts' );

/**
 * Enqueue scripts (or styles) conditionally.
 *
 * Load scripts (or stylesheets) specifically for IE. IE10 and above does
 * not support conditional comments in standards mode.
 *
 * @link https://gist.github.com/wpscholar/4947518
 * @link https://msdn.microsoft.com/en-us/library/ms537512(v=vs.85).aspx
 */
function enqueue_my_styles_and_scripts() {

     // Internet Explorer HTML5 support
    wp_enqueue_script( 'html5shiv',get_template_directory_uri().'/js/html5shiv.js', array(), '3.7.3', false);
    wp_script_add_data( 'html5shiv', 'conditional', 'lt IE 9' );

    // Internet Explorer 8 media query support
    wp_enqueue_script( 'respond', get_template_directory_uri().'/js/respond.js', array(), '1.4.2', false);
    wp_script_add_data( 'respond', 'conditional', 'lt IE 9' );

}

You can use conditional operators in WordPress to enqueue scripts on specific pages of your Website.

function load_script_for_single_post(){
    if(is_single()){
        wp_enqueue_script(
                'some',
                get_template_directory_uri().'/js/some.js',
                array('jquery),
                '1.0.0', 
                false
        );

    }
} 
add_action('wp_enqueue_scripts','load_script_for_single_post');

In the above example, if the current webpage is single post, script will be enqueued. Otherwise wp_enqueue_script function will not be executed.