As someone who enjoys computing history, this has been a question I've had for a long time. The Internet didn't seem to have a definite answer for this, only lots of speculation and different authoritative answers. I've spent several days trying to track down as many primary sources as I can.

The quick and definitive answer (as a TL;DR): Cron comes from chronos (Greek word/prefix for time), misspelled as cron by author Ken Thompson.

The other possibilities that were ruled out:

• CReate On utility (acronym), first published 1988
• Chronos (Greek god for time), first published 1993
• Command Run On Notice (acronym), first published 1994
• Commands Run Over Night (acronym), first published 1997

Here are the details of the timeline I found:

• Cron first appeared in Unix V6, written by Dennis Ritchie and Ken Thompson. The source code
  [1]
  doesn't detail much in the form of comments, but the man pages dated Oct 25, 1974 mentioned "clock daemon" with no explanation of why it was named cron.

Screenshot from a nice PDF version of the original ASCII file.

• Later on Steve R. Sampson posts to the comp.os.minix Usenet group on Feb 14, 1988
  [2]
  , his own source code for a MINIX cron with comments mentioning it was a "CReate On Utility". A user's hard copy of a CTIX (MegaFrame) manual
  [3]
  from that time-frame also mentions "CReate On Utility". Given MINIX and CTIX were quite separate recreations of Unix at the time, from scratch modeled after V7
  [4]
  and from Unix System III respectively, the fact that both of them were consistent made this option seem very probable. There are many other examples of Unix commands/files that are formed from two words by concatenating a short prefix of the first word to the second (e.g. chmod, chown, cref) or using two characters for the first word (e.g. mkdir, rmdir), and so cron didn't seem unreasonable. These are also the earliest primary sources online that have actually explained the acronym clearly and officially.

• By May 18, 1993, the Unix Acronym List compiled by Wolfram Rösler posted to comp.unix.misc
  [5]
  lists cron as being an acronym of Cronos (sic), and subsequently corrected to Chronos (greek god). (This list is actually still maintained online by Wolfram on his website with this definition unchanged.)

• In an AUUG conference in September 1994
  [6]
  , as found by Wikipedia user Xavier, cron was explained as "command run on notice".

• In 1997, Beginning UNIX
  [7]
  was published by Mike Joy with a probable explanation of "commands run over night" (also found by Xavier).

I was ready to conclude that CReate On Utility was the rightful explanation, but the 14 years difference between inception in 1974 and documentation in 1988 wasn't very satisfactory. So I took Erik Fair's advice here and went to ask Prof. Brian Kernighan, who is widely attributed to be the author of cron, directly. He's a professor at Princeton now and still teaching even in 2015, and would probably respond to a nicely worded request. His response would then be able to quell all speculation forever.

And discovered that:

• He does respond really quickly and helpfully! I got a response in less than 2 hours this very afternoon.
• He wasn't the author of cron -- but Ken Thompson was.
• And there you have it, Ken's definitive answer: it comes from the Greek prefix for time, and that it would have been chron if he could spell! :)

Quoted with permission.

As a sidenote, it is interesting to note that the computing term daemon also had a similar misconception, or backronym/retronym, early on. It was thought to stand for Disk And Execution Monitor, but actually just came from the regular word daemon (of "Maxwell's daemon").

Prof. Fernando J. Corbato and Prof. Jerome H. Saltzer, from the original team at Project MAC using the IBM 7094 in 1963, as posted on Take Our Word For It, page four, Sez You...:

Your explanation of the origin of the word daemon is correct in that my group began using the term around that time frame. However the acronym explanation is a new one on me. Our use of the word daemon was inspired by the Maxwell's daemon of physics and thermodynamics. (My background is Physics.) Maxwell's daemon was an imaginary agent which helped sort molecules of different speeds and worked tirelessly in the background. We fancifully began to use the word daemon to describe background processes which worked tirelessly to perform system chores.

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