Apple - Change background colour for PDF when Viewing

So Preview does not have this feature, but more on that in a moment.

f.lux

I would strongly recommend you take a look at f.lux.

f.lux makes your computer screen look like the room you're in, all the time. When the sun sets, it makes your computer look like your indoor lights. In the morning, it makes things look like sunlight again.

f.lux will adjust (you can modify the strength) the colour of the whole screen to make it easier on your eyes. You can set it to be on all the time, or automatically come on at night time. People love it.

Now, back to your question...

Adobe Reader for Mac does support this. Once you install the 400MB app, you can change the background colour in Preferences (⌘ cmd + ,) > * Accessibility** . Check Replace Document Colours, and set the right colours you want.

You can change the background color in Skim (a popular and lightweight app for viewing, highlighting, annotating, and editing PDFs). Open up your document in Skim, then open up the (Apple) Script Editor (search script in the spotlight search), paste the following script in there and run it:

tell application "Skim"
    set theColor to choose color
    set page background color to theColor
end tell

This opens up the Skim color chooser from which you can choose your desired background color. Unfortunately the changes are not persistant. So for easier changes in future, save the script (the Script Editor's default saving location is iCloud), and then for subsequent changes all you have to do is to open the scirpt editor, double click the script, and run it. See Here for more details.

Please note that if you change the background color using the Skim UI, only the surrounding color changes, rather than the document's background color.