Introduction
In the 50 years since Marvel officially debuted the concept of mutants, there have been hundreds upon hundreds of these types of characters created, spreading out across most of Marvel’s line of comics. You would think the answer of who was the first one would be simple… but the answer changes, depending on how you want to look at the question. The article will help examine the various candidates based upon publication dates, as well as in-universe criteria to identify possible answers.
Who was the first mutant…born?
For many years, the answer to this question was simple: Apocalypse. Debuting in X-Factor (1st series) #5, his backstory was fleshed out to reveal that he was born in ancient Egypt around 3000BC. This premise was carried over into many other media forms, such as the various X-Men cartoon series and even a film. However, in X-Force: Necrosha, new information was revealed that showed Selene, the Black Queen, was the first mutant, having been born in 15,000BC, some twelve-thousand years before Apocalypse.
Selene was no stranger to the X-Men at this point, having debuted over 25 years earlier in New Mutants (1st series) #9. Her early appearances hinted at her possible longevity, as her mutant power was the ability to drain other people’s life force to maintain her youth. Her fascination was ancient Rome was also a key indicator that she was much, much older than the youthful beauty of her face indicated.
Sometimes, when information is relayed from a character, the reader cannot always trust the words they are saying. However, in this case Selene was actually shown as a baby on-panel with a captioned date attached, which is much harder to dispute. So, for this question, that answer is rather simple and easy to identify. Selene was the world’s first mutant and also holds the record as being the oldest, as she is still very much alive.
As Selene proved, though, any character can be written as being even older, so how long she holds this crown for is anyone’s guess.
Who was the first mutant… published?
This is the question that gets trickier, as there are a number of legitimate answers to this. You would think the answer would be straight-forward, as the X-Men (and Marvel’s mutant race in general) debuted in X-Men (1st series) #1 in 1963. Later issues would narrow down the definition of being a mutant to a person who possess the X-gene. This clarification is important, as the word mutant was thrown around in comics beforehand but, until the X-Men first debuted, it had never knowingly been attributed to an actual sub-species before.
During the 1950’s, a number of comics were published by Marvel, then known as Atlas Comics, that used the term “mutant.” Amazing Detective Comics #11 (1952) and Man Comics #28 (1953) both had characters with superhuman abilities that identified themselves as mutants. Other examples popped up during the rest of the decade, sometimes using the word mutant or sometimes just mimicking the conditions that caused their powers to develop.
However, in 1962’s Amazing Adult Fantasy #14, Tad Carter debuted, a normal looking boy who suddenly found he was telekinetic and could read minds. Tad is special because he would also make appearances after the introduction of the X-Men and was officially confirmed to be an X-gene possessing mutant. So, although the X-Men were the first to use the modern classification of mutant, Tad Carter actually appeared on page over a year before them. None of the other characters who were referred to as mutants who had appeared previous comics ever appeared again. So we cannot say for certain whether they really were mutants or they just used that label liberally.
To make things even more complicated, you have to consider Namor the Sub-Mariner. First appearing in 1939’s Marvel Comics #1 (after a preview in Motion Picture Funnies Weekly #1) produced by Timely Comics, Namor was revealed to be an Atlantean, another sub-species of the human race. Along with the likes of Captain America and other heroes of the time, he became one of Timely Comics' first superheroes. Many of the superheroes fell out of favor during the 1950’s and it wasn’t until the resurgence of superhero books with the likes of the X-Men, Fantastic Four and Avengers during 1961-1963 that they 
appeared again. Namor popped up again, though in a more anti-hero role, and he soon crossed paths with the X-Men. In X-Men (1st series) #6, it was strongly indicated that many of the powers Namor possessed were actually attributed to him being a mutant. Later comics would go on to solidify this theory and establish that Namor was in fact a mutant, born to a human father and Atlantean mother. In 1990 Marvel embraced Namor's heritage by adding the tag "Marvel's First and Mightiest Mutant" to his series Namor, the Sub-Mariner. It would still be another 19 years until Namor officially joined the ranks of the X-Men, embracing his mutant heritage. Marvel further canonized this fact by releasing a series titled Namor: The First Mutant.
So, much like Tad Carter, whilst Namor was not classed as an X-gene carrying mutant on his debut, retroactively he can be called one.
Conclusion
Publication-wise, there are a number of answers to the question questions of who was Marvel’s first mutant. Professor Xavier, the original five X-Men and Magneto all appeared in X-Men (1st series) #1 making them the first confirmed X-gene carrying mutants Marvel published. However, Namor was retroactively classed as one and he first appeared in 1939, some 23 years before the X-Men. Then there are the characters from the 1950’s, who were never shown to be carrying the X-gene but were still called mutants at the time.
As demonstrated, simply referring to the “first mutant” is a complicated matter but hopefully this article has enlightened you on the history and arguments. Who you chose to side with is all up to how you perceive the question.