Is it possible to be admitted to CS PhD programs (in the US) with scholarship at age 18?

[For context: I am a professor of mathematics at the University of Georgia. I've served on my department's Graduate Committee, which does graduate admissions, for about eight years. From 2016-2019 I was the Graduate Coordinator, hence the faculty member most directly involved in the graduate admissions process.]

Regarding your son, you told us:

1) He is a junior studying CS at well-known university. He has perfect grades and GRE scores, and he has multiple first authored papers in highly ranked journals and conferences.

2) He is 16.

To my mind, the first point is highly relevant. In mathematics a student with that profile would probably get into some of the top PhD programs in the country. I am confident that the same holds in CS. Moreover, in both of these fields, admission to a top program comes with full funding the vast majority (over 95%) of the time.

I am also assuming that since your son is 16 now and in his junior year, he will be 18 -- i.e., an adult -- when he starts graduate school. Given this, the second point does not seem relevant to me. Some people will find your son's achievements (even) more impressive given his age. Others will have some concerns about the maturity and readiness of such a young student for a PhD program. But when it comes to admissions and hiring, times have changed: in the last few years faculty have received much more training and specific instructions (including on legal obligations) regarding admissions and hiring than in years past. Deciding not to admit a qualified student because of his age sounds like a discriminatory practice to be avoided. Conversely, giving more weight to a student because of his age sounds like a discriminatory practice against the other applicants...also to be avoided. A small number of committees may still be influenced by such thinking, but overall it should be the case that your son will be considered only on point 1) and I think that it will be the case.

In summary: your son has an excellent profile that will most likely lead to multiple fully funded offers at prestigious CS programs in the US. (By the way: yes, he should apply directly to a PhD program.) You do not need to, nor do I think you should, do anything out of the ordinary because of his age.

I strongly recommend that your son (or you) speak with the professor he is working with at his university for guidance on your questions. With that being said...

With regards to funding age restrictions, it should not be an issue. Also, funding for CS PhD programs (at least in the United States and Cananda) is almost always guaranteed with acceptance and is thus not a separate competitive process. For example, University of Toronto's CS PhD program explicitly states guaranteed funding periods with acceptance (link: https://web.cs.toronto.edu/graduate/about). There are other sources of funding that are competitive, such as the United States' NSF Graduate Research Fellowship, and do not have age eligibility requirements; however; the NSF Fellowship I just mentioned is restricted to US citizens.

The other answers speak effectively to the general case, and I agree with them, but thought an answer focusing on the specifics might be relevant too.

I suspect you are already aware of the strong parallels between your son's case, and that of another Canadian student with an interest in computer science, Erik Demaine, who was admitted into a funded PhD program in computer science at the age of 14, and went on to become MIT's youngest ever faculty member. Admittedly this was in Canada, but it would be difficult to imagine a US school turning down a similar opportunity.

If funding is a concern, your son may also want to look into fellowships and scholarships. If your son is a US Citizen, he may be competitive for an NSF Graduate Fellowship.

It sounds like your son may only have Canadian Citizenship however. Luckily, NSERC provides two sources of funding that your son can take with him to a US School: The PGS-D award, and the MSFSS award. The PGS-D, as I recall, can be taken at an institution outside Canada. The MSFSS award can be used to cover the cost of an exchange, rather than a permanent position.