There is a big difference in these functions. Actually both functions perform the same task which includes the file but the process of including the file a quite different.
This function include the file and make sure that same file will not get included again.
For example if your file say function.php have one function test.
This function also include the file regardless of checking the inclusion of the file in previous code.
If you know what you are doing then its better to use include.
Note: include_once() will check for whole code to check the existance of the file, So its better to use include() over include_once().
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