Is there any Biblical reference strictly speaking about God being timeless? I've heard a lot, mainly from apologists, the notion that God is Timeless (Little example). So, this is an assumption on the philosophical ground, but is there a theological ground for it? Any verse in the scriptures that talks about His relatioship with time, or we can assume that He is timeless just because He is the Creator of everything and He is Eternal?
While how much philosophy has influenced the church on this can be debated,  one only has to look to Scripture to see that God clearly operates outside time. 

The term "outside time" may mean different things to people. To to clarify I'm saying that in order to be considered outside time one must display the ability to 


Control time.
Independent of time, not bound by its linear restrictions.
Understand and perceive events in time, if not time itself, in a way that is,  again,  not restricted by the laws of time as they apply to us.


Creation

First,  we have the idea that God created the universe. As physics has advanced we have learned more and more how time is an integral part of our universe, tied together with how it operates. So when God created the universe it seems plain that he created time as well.  And if he has dominion over all creation,  then that would include time.  This may be the simplest and yet strongest argument. 

Controlling Time

If that seems to be too much philosophical reasoning,  which may or may not be influenced,  then consider what scripture has to say. 

We see in Joshua 10 that the sun and moon stopped. Now,  time still passed in some way, allowing the Israelites to continue the fight,  but this shows extreme control over creation.  Many speculate that the only way to do such a thing without causing a massive cataclysm to the entire solar system would be to actually stop time around the Israelites,  or to accelerate it so it seemed it stopped around then.  

Either way,  there is control of time in the ability to stop,  slow,  accelerate time simply violate physics entirely without damage. 

A similar event happens in 2 Kings 20 when God moves the shadow backwards as a sign to Hezekiah. 

Independent of Time

The OP seems to accept God's eternal nature. To be eternal is to be independent of time. It has no effect on him as he never changes.
Psalm 90 has much to say including in verse 2:


  from everlasting to everlasting you are God.


Perceiving Events from Outside

We also see prophecy in scripture where God has clear knowledge of our future as if it was the past. 

Isaiah 46:9-10 


  I am God, and there is none like me,10 declaring the end from the beginning and from ancient times things not yet done,


Isaiah 48:5 


  I declared them to you from of old, before they came to pass I announced them to you,


Psalm 139:16


  Your eyes saw my unformed substance;
  in your book were written, every one of them,
  the days that were formed for me,
  when as yet there was none of them.


Also it seems time does not pass for God the way out does for us. 

2 Peter 3:8


  But do not overlook this one fact, beloved, that with the Lord one day is as a thousand years, and a thousand years as one day.


Conclusion

There is lots of internal evidence in scripture,  if you accept it on its own merit,  that suggests that God is independent, in control, and able to perceive all of time.