I had this issue with pretty permalinks myself, and the solution was to edit my vhosts conf file for that site. Here’s what worked for me:

<VirtualHost *:80>
    ServerAdmin webmaster@localhost
    ServerName broseph.com.au

    DocumentRoot /var/www/broseph.com.au/public_html
    <Directory />
        Options FollowSymLinks
        AllowOverride None
    </Directory>
    <Directory /var/www/broseph.com.au/public_html>
        Options Indexes FollowSymLinks MultiViews
        AllowOverride All
        Order allow,deny
        allow from all
    </Directory>

    ErrorLog ${APACHE_LOG_DIR}/error.log
    CustomLog ${APACHE_LOG_DIR}/access.log combined

</VirtualHost>

• Also make sure your .htaccess file has the proper permissions for WP to write to it. You’ll see an error if it doesn’t.
• FYI: conf files are in /etc/apache2/sites-available
• Don’t forget to restart apache after editing the conf file: sudo service apache2 restart

My issue was from making the update from Ubuntu 12.04 to 14.04 was that my apache2.conf was not correct configured:

In terminal type:

sudo gedit /etc/apache2/apache2.conf

Find:

<Directory /var/www/>

And make sure the AllowOverride directive is set to All.

After I made that change I could use custom permalink structures in Wordpess again, hope this helps anyone as it did me!

you have to enable moderewrite.c for apache
more info
after enable moderewrite , make sure you have .htaccess file in the public_html :

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>

# END WordPress

and restart the apache server

sudo service apache2 restart

I was having a similar issue. The website would work on the home page and I could log into WordPress admin, but if I clicked on any other link it resulted in a 404 error.

The page that is linked to in some of the other answers isn’t the ideal solution. Basically, it turns on AllowOverride to “All” which allows .htaccess files to work. This is great when you are on shared hosting with no access to the apache configuration file, but shouldn’t be used when you are on a host such as digitalocean, where you have access to the server configuration file.

The ideal solution is to put the information that is in the WordPress .htaccess file into the main apache configuration file. This helps to improve the server performance. This page shows how to do it and why: http://haydenjames.io/disable-htaccess-wordpress-performance/

Thank you!

Thank you so much! XD