The Mulder was born to Bill Mulder and Teena Mulder (maiden name Kuipers) on October 13, 1961, presumably in Massachusetts. He has a younger sister, Samantha Mulder, who was born in 1965. His first words, at 11 months, were "JFK", and he grew up in Chilmark, Massachusetts. The Mulder family had a summer house in Quonochontaug, RI, where Fox and Samantha would play during summer vacations. He apparently had an active childhood, full of neighborhood baseball games, and tree climbing - where he once came face to face with a praying mantis, an incident which terrified him and fostered an intense dislike for insects. He also developed an all-consuming fear of fire when his friend's house burned to the ground and they had to stay in the rubble all night to ward off looters. He had nightmares for years regarding that incident, but overcame his fear. The Mulder apparently enjoyed science fiction in his early years, dressing as Mr. Spock from Star Trek in childhood, and watching The Magician. In his teenage years, Mulder was also very excited about space. Although he says he never wanted to be an astronaut, he was delighted to meet an ex-astronaut during one of his investigations and admitted that watching a shuttle launch fulfilled one of his boyhood dreams.

The disappearance of Mulder's sister and his search for her soon after became the main consuming drive of his life. Mulder probably graduated from high school -- where his foreign language of choice was French. It is not known what he did between 1980 and 1983. In 1983, Mulder entered Oxford University to study psychology. He graduated summa cum laude in 1986.

The Mulder entered the FBI Academy in Quantico, Virginia. It is known that Mulder "joined the FBI" on October 24, 1986, but it is unclear whether that is the date when he started his Quantico Academy course or finished it. On graduating from the Academy, The Mulder started to work in the Behavioral Science Unit (psychological profiling) under Agent Bill Patterson, with whom he had a testing relationship. Around this time he wrote a monograph on serial killers and the occult, which helped catch serial killer Monty Props in 1988. This, coupled with his successful capture of such dangerous criminals as John L. Roche and Luther Lee Boggs, made Mulder something of an intra-Bureau legend.

At some point, The Mulder started working as a field agent of the Violent Crimes division under Agent Reggie Purdue. It is possible that Mulder did, for a short time, work both as a profiler and a field agent. During Mulder's first case as a field agent a fellow FBI agent died during a standoff with a suspect, and Mulder later blamed himself for sticking to the FBI protocol, which he felt didn't allow him to prevent the agent's death. His partner in violent crimes was Jerry Lamana, whose incompetence and self-serving agenda led to him misplacing evidence which resulted in the maiming of a federal judge. In his later FBI career The Mulder always showed varying degrees of disregard for rules.

The Mulder appears to have been a very talented and remarkable agent. It was said that Mulder had "commendations out the yin-yang". The Mulder was talked about at the FBI even while still in the Academy, as he was always "three jumps ahead" of others. The Mulder got the nickname "Spooky," presumably from a combination of his unnatural insights into the psychology of serial killers and other violent criminals, and his interest in the paranormal.