Your Code

Your code must have something like:

function foo(){
    if(document.hidden){
        //do something
    } else {
        //do something else
    }
}

Well, what’s the problem with that?

The Problem

You are using a global property. How are you planning to test this? Try this:

it("should not work", function(){
    document.hidden = mockValue;
    foo();
    expect(...).toBe(...);
});

First, this doesn’t work for browser’s global properties (on window or document), But even for your own global properties (which you really should try to avoid…), it is really bad practise. What if you fail to remember to return the correct value?

Let’s say that your’e using global functions. This is less bad:

function foo(){
    window.blur();
}

Why? because you can spy on functions:

it("should call window.blur()", function(){
    spyOn(window, 'blur');
    foo();
    expect(window.blur).toHaveBeenCalled();
});

So, what to do?

Better Code

If you’re using a framework such as angularjs, you should use the provided wrapper. In angular it is $window. Now, since angular is based on dependency injection, you can easily inject your mocked object.
But what to do for vanilla?

function getDocument(){
    return window.document;
}
///
function foo(){
    if(getDocument().hidden){
        //do something
    } else {
        //do something else
    }
}

Now, you can test your BL:

it("should work now", function() {
    spyOn(window, 'getDocument').and.returnValue(mockDucument);
    mockDucument.hidden = mockValue;
    foo();
    expect(...).toBe(...);
});

Basically, you’ve changed your code use DI (dependency injection), and now your code is testable.

Wait, Should I change my code just for a test?

Yes.
Your code is bad. You’re not changing it, you’re fixing it.
Testable code is better code.