Khalifa was born in Egypt on November 19, 1935.
Khalifa obtained an honors degree from Ain Shams University, Egypt, before he emigrated to the United States in 1959, later earning a Master's Degree in biochemistry from Arizona State University and a PhD. from University of California. He became a naturalized U.S. citizen and lived in Tucson, Arizona.
Khalifa worked as a science adviser for the Libyan government for about one year, after which he worked as a chemist for the United Nations Industrial Development Organization, then became a senior chemist in Arizona's State Office of Chemistry in 1980.
He was central to the founding of the United Submitters International, (USI), an offshoot Islamic group. He coined the phrase "Final Testament" in reference to the Quran.
Khalifa said that he was a messenger of God and that the archangel Gabriel "most assertively" told him that chapter 36, verse 3, of the Quran, "specifically" referred to him. His followers refer to him as God's Messenger of the Covenant. He promoted a strict monotheism and was a prominent Quranist, rejecting the hadith and sunnah as fabrications attributed to Muhammad by later scholars.
He wrote that the Quran contains a mathematical structure based on the number 19. Starting in 1968, Khalifa used computers to analyze the frequency of letters and words in the Quran. In 1974, he claimed that he had discovered a mathematical code in the text of the Qur'an involving the number 19. The details of this analysis are available in his book, Quran, the Final Testament.
Khalifa's research did not receive much attention in the West. In 1980, Martin Gardner mentioned it in Scientific American. Gardner later wrote a more extensive and critical review of Khalifa and his work.
Khalifa's first publicized report in the Arab world appeared in the Egyptian magazine Akher Sa'a, in January 1973. Updates of his research were subsequently published by the same magazine later that year and again in 1975.
In October, 1979, Khalifa was accused of sexual assault, sexual abuse, and sexual contact with a minor. The accuser, a 16-year-old-girl, testified at a hearing that Khalifa sexually molested her while recruiting her for research on the human aura. There was no evidence of intercourse found when the girl was examined at a local hospital. Justice of the Peace James P. West ruled there was probable cause to hold Khalifa for trial on the charges.
On January 31, 1990, he was found stabbed to death inside the Masjid (Mosque) of Tucson Arizona, his place of employment. He was stabbed multiple times. Nineteen years after the murder, on Tuesday, April 28, 2009 the Calgary Police Services of Canada arrested Glen Cusford Francis, a 52-year-old citizen of Trinidad and Tobago, on suspicion of killing Rashad Khalifa. Investigators in Tucson learned that Francis, who was going by the name Benjamin Phillips, had begun his studies under Khalifa in January 1990. Phillips disappeared shortly after the slaying, and was said to have left the country. An investigation revealed Phillips and Francis were the same man upon discovering fingerprints found in Phillips' apartment. A specialty unit of the Tucson Police Department progressed in its investigation in 2006 and in December 2008 and was able to use DNA testing on forensic evidence from the crime scene to tie Francis to the assassination. In October 2009, a Canadian judge ordered his extradition to the United States to face trial. The trial for the assassination began on December 11, 2012. On December 19, the jury, after a three-hour deliberation, found Glen Francis guilty of first-degree murder.
Prior to the Francis trial, James Williams, an alleged member of the Jamaat ul-Fuqra organization, was convicted of conspiracy in the slaying. Williams disappeared on the day of his sentencing and could not be found. In 2000 Williams was apprehended attempting to re-enter the United States and sentenced to serve 69 years in prison. His convictions were upheld on appeal by the Colorado Court of Appeals except for one count of forgery.
CBS News reported that Muslim extremist Wadih el-Hage was "connected to the 1990 stabbing death... El-Hage, who was indicted for lying about the case, called the assassination 'a good thing.'" If he was really involved in it, Khalifa would be possibly the first American killed by an operative of Al Qaeda in the United States.