As examiner for the Smith's prize, he appraised the early work of G. G. Stokes, Arthur Cayley, John Couch Adams, William Thomson (later Lord Kelvin), Peter Guthrie Tait and James Clerk Maxwell.

Challis finally began his, somewhat reluctant, search in July 1846, unaware that Frenchman Urbain Le Verrier had independently made an identical prediction.

German astronomer Johann Gottfried Galle, assisted by Heinrich Louis d'Arrest, finally confirmed Le Verrier's prediction on 23 September.

It soon became apparent from Challis's notebooks that he had observed Neptune twice, a month earlier, failing to make the identification through lack of diligence and a current star chart.

[2] Challis was full of remorse but blamed his neglect on the pressing business of catching up on the backlog of astronomical observations from the observatory.

As he reflected in a letter to Airy of 12 October 1846:[4] I have been greatly mortified to find that my observations would have shewn me the planet in the early part of August if I had only discussed them.

I delayed doing this ... chiefly because I was making a grand effort to reduce the vast numbers of comet observations which I have accumulated and this occupied the whole of my time.

Driven by Sir Isaac Newton's somewhat obscure assertion of "a certain most subtle spirit which pervades and lies hid in all gross bodies",[5] Challis was driven to attempt to derive all physical phenomena from a model of inert spherical atoms embedded in an elastic fluid ether,[6] an enterprise described as an attempt at a "Victorian unified field theory".

Challis saw Genesis as an "antecedent plan" for creation, rather than a literal chronology, and argued that the biblical account could be reconciled with the geological record.

However, despite his tenacity in advocating his physical and theological theories, they had little impact,[2] and in fact Richard Carrington credited him as his professor with inspiring his decision to pursue astronomy rather than become a clergyman.