Yes.
Of course, a question as broad as that can be answered in any number of ways, so I’ll elaborate.
Vitamin D3 is more biologically active than vitamin D2 in humans as well as many other animals. As far back as the 1930s, scientists have observed that supplementation with significantly greater amounts of vitamin D2 were required to match the effects of vitamin D3.
The activity is actually greater for each “level” of vitamin D.
Vitamin D3, starting out as cholecalciferol, is more easily converted to 25[OH]D than vitamin D2 (ergocalciferol) is. 25[OH]D in the blood is the best predictor of vitamin D sufficiency (in patients without conditions preventing them from further metabolizing vitamin D, such as renal failure).
The final (and absolutely critical) “level” of vitamin D is more active as 1,25[OH]D3 than as 1,25[OH]D2. In this case, the vitamin D2 form is sometimes considered “better” as the more active form carries a greater risk of toxicity for parathyroid and renal patients requiring 1,25[OH]D supplementation.
Vitamin D3 is also arguably the most natural form. Cholecalciferol is produced naturally in human skin exposed to sufficient levels of UV-B radiation. This is the form of vitamin D we have been using for millennia, whether it’s been vitamin D3 synthesized in our skin or obtained from a diet rich in oily fish.
Research on vitamin D is constantly expanding. We have discovered vitamin D receptors in the cells of most of our tissues. We are constantly learning more about how vitamin D works on the molecular level — even as research continues to turn over new and previously unsuspected relationships between vitamin D and things like depression, immune health, and alzheimers. If there is a natural place for vitamin D in these processes, it seems as though vitamin D3 would better fill that place. After all, we only really started consuming vitamin D2 less than a century ago!
To read more about why vitamin D2 and D3 are often treated as the same thing and the extensive research that has been done distinguishing the two, check out this article:
The case against ergocalciferol (vitamin D2) as a vitamin supplement