The best method, I find, is this. Let’s say you want MATLAB to start up in mystartupdir, and you’ve placed startup.m in that directory.
On Windows, make a shortcut icon to MATLAB, then right-click on it and select Properties. Edit the field Start In. Now, use this icon whenever you want to start MATLAB.
On other platforms, you can run MATLAB with the -sd flag to specify the startup directory:
matlab -sd mystartupdir
If you don’t specify a startup directory, MATLAB will use the default specified by the userpath command. You can place your startup.m file there.