This problem usually occurred when you upgrade the version of Cpanel. In order to resolve this problem follow the steps given below:-

1) First you will need to check the permission for files
/usr/local/cpanel/3rdparty/bin/php
/usr/local/cpanel/3rdparty/bin/php-cgi

2) Above both files should have 755 permissions, If it is not 755 permission then change the permission to 755.

3) Once the permission is changed run the below command from shell
/scripts/makecpphp

Now you will not receive phpMyAdmin “500 internal server error”.