The battery on my 1994 XJS went flat over the winter. I put it on charge in the car and there is a loud clicking noise coming from under the hood. Car will not start if the battery charger is switched to ‘start’ mode.
Have you determined from whereabouts under the hood?
That’s a big area down in there, and it is packed full of engine. 
clicking could be the starter motor relay engaging , without enough power to turn the engine
Remove the battery and take it to an autoparts store to be tested. Depending on the age of the battery and how much it was depleted it may not hold a charge. If the battery is bad get a new one, install it, and see if your cars starts as it should.
Consider getting a knife switch for easy battery disconnect like I did with our 1990 XJ-S convertible.
Paul
If battery is less than 6 years old, put it on a charger overnight, it may just need a good charge up. And do what Paul said if you store it for winter, a simple way to disconnect.
Batteries are good for about 3-4 years…the companies here guarantee them for one or two years…don’t pro rate them anymore…that tells me something…so. I. Don’t run batteries for six or seven years like you once could.
That was my first thought too, but that would require the key to be in the “start” position, or something being damaged (ignition switch, starter relay, a wire someplace, etc), thus my question as to “where” the noise was.
That part of the question could be the battery, but first: is the clicking noise with the key in “start” or when the charger is connected, as was described?
I just replaced the Sears Diehard Gold, that was made in 9/18, in our 1990 V12 Vanden Plas (5.3L V12 with Lucas ignition like many XJ-Ss) when the starter cranking was very slow even after having a float charger connected overnight. I also noticed that the trip computer reset on start a few times unexpectedly.
I got 5 1/2 years of regular use out of this battery while living in the mild climates of southern California and now South Carolina. This car rarely sat for more than a month at a time and was driven an average of about 3,000 miles a year over the past 12 years. I have never parked it for months at a time. I think the face-lift cars (1992-1996) are more prone to battery issues due to the high parasitic load of all the additional electrical equipment.
Paul