First observed as a faint telescopic object on 18 September 1965, the first calculations of its orbit suggested that on October 21, it would pass just 450,000 km (280,000 mi) above the Sun's surface, and would probably become extremely bright.

The three pieces continued in almost identical orbits, and the comet re-appeared in the morning sky in late October, showing a very bright tail.

Comet Ikeya–Seki was independently discovered on 18 September 1965 by Japanese amateur astronomers Kaoru Ikeya and Tsutomu Seki within roughly 15 minutes of each other.

Based on preliminary estimations of Ikeya–Seki's orbit, Fred Whipple of the Smithsonian Astrophysical Observatory conjectured that Ikeya–Seki was a sungrazing comet.

[10] Nonetheless, Ikeya–Seki's increasing luminosity remained apparent;[8] in the Southern Hemisphere, where visibility of the comet was most favorable around the time of perihelion, observers reported Ikeya–Sekit to be as bright as magnitude 0 by 18 October.

[8] The two components of Ikeya–Seki's fractured nucleus remained apparent with increasing visual separation, moving apart at approximately 14 m/s (31 mph); one was brighter but more diffuse in appearance than the other.

[14] Observations obtained by the McMath–Pierce solar telescope at Kitt Peak National Observatory detected emission lines associated with ionized calcium, chromium, cobalt, copper, iron, manganese, nickel, sodium, vanadium, and cyanide in Ikeya–Seki's coma.

A Convair 990 operated by NASA out of Hawaii and a Boeing 707 with scientists from Los Alamos National Laboratory were also involved in observational efforts targeting Ikeya–Seki.

Gemini 6A was also planned to incorporate observation of the comet until the loss of the Agena target vehicle led to the cancellation of the original mission.

Elizabeth Roemer remarked of the breadth of observational data in Publications of the Astronomical Society of the Pacific that "There seems no doubt that the appearance of Comet Ikeya–Seki will stand as a landmark in cometary physics.