Short answer: the smell is almost never the toilet. It is the water sitting in the bottom of the brush holder. The brush comes out of the bowl soaked, goes into a closed cup, and the water runs down and pools. Dark, damp and airless is exactly what bacteria want, and after a few weeks the holder smells worse than the toilet ever did.
Here is how to clear it today, and the three ways to stop it coming back.

Why it smells
Three things have to be true for a bathroom to smell of old water, and a closed brush holder gives you all three at once.
There is water, running off the bristles every time the brush goes away wet. There is something for bacteria to feed on, carried down with it. And there is no airflow, because the holder is a cup with a brush sitting in the mouth of it.
This is the point cleaning writers keep making: putting a wet brush straight into a dark, closed container is what breeds the problem, and a holder that lets air move is the usual advice (Clean Mama, reported by AOL).
The ten-minute fix
- Tip the water out into the bowl. Not the sink.
- Clean the brush over the bowl. Hold it above the water and pour bleach or a bathroom disinfectant down through the bristles. Molly Maid's advice, via Family Handyman, is to do this every single time you use it, and to mix bleach fresh, because it loses its strength within about a day.
- Soak it once a week. Bleach for an hour, or white vinegar for thirty to sixty minutes. The holder goes in too. That is where the smell actually lives.
- Dry it properly. This is the step everybody skips. Rest the handle under the closed toilet seat so the head hangs over the bowl and drips. Give it a couple of hours. A damp brush going back into a holder has started the clock again.
- Dry the inside of the holder before the brush goes back in it.

Why it comes back anyway
Because that fixes the brush, not the design. A closed holder rebuilds the puddle the next time you clean the toilet, and almost nobody is going to hand-dry a toilet brush every week for the rest of their life. That is not laziness. It is a fair reading of how much attention a toilet brush deserves.
When the brush is past saving
Replace it about every three months if you only rinse it, and every six to twelve months if you genuinely disinfect it weekly. Sooner if the bristles have splayed or gone flat, if the staining will not shift, if it still smells after a clean, or if you can see mould (guidance from cleaning professionals).
A flattened brush is worth replacing on performance alone. It pushes dirt around the bowl instead of lifting it off.
The three real fixes
1. Store it in the open
A ventilated holder, a hook on the side of the pan, a jug you do not want back. Free if you already own something suitable, and it solves the airflow problem outright.
The catch: nothing catches the drips on the walk from bowl to holder. You have traded a smell for a trail across the floor.

2. Disposable wand heads
A handle with a throwaway head on the end. There is no wet brush to store at all, which is the most complete answer to the question.
The catch: you buy refills forever, and a soft disposable head is not the tool for a ring that has been sitting there a while.
3. A brush that carries its own tray
The drips are caught at the bowl, before the brush moves anywhere, and the tray is open enough to dry. This is the one we make, so read the next part knowing that.

When ours is the wrong call
Skip it if you already rinse and dry your brush after every use. That works, and paying for a tool to do a job you are already doing is a poor trade.
Skip it if what you really want is no brush at all. Buy the disposable system instead.
Skip it if your current brush is a month old and perfectly good. Store it in the open and see whether that alone fixes the smell.
It is the right call when the drips across the floor are the part you actually hate, and you would rather the problem was designed out than managed every week.
The brush in this article

How it works: the button releases the caddy so it swings out of the way while you scrub, and you fold it back while the brush is still over the bowl, so it catches everything that runs off.
The ELYPRO Drip-Free Toilet Brush is patented in the United States, number 11,457,777. The caddy is ventilated so it dries between uses, and it has a spout, so whatever it catches pours straight back into the toilet. Heavy-duty ABS, firm non-shedding bristles that reach under the rim.
$24.99. Rated 4.86 out of 5 across 42 reviews. Picked by Good Housekeeping, and named in House Digest's list of the 15 best toilet brushes.
See the Drip-Free Toilet Brush · All ELYPRO bathroom
Questions people ask
Does the smell mean my toilet is dirty?
Usually not. Lift the brush out and smell the holder on its own. If that is the source, the bowl is not your problem.
Is a silicone brush more hygienic?
A silicone head has fewer places for debris to lodge than a tuft of bristles, and it sheds water faster. What it does not change is where the brush goes afterwards. If the holder is still a closed cup, you will still get the puddle.
Can I keep bleach in the holder between cleans?
There is little point. Bleach loses its strength within about a day, so by midweek you have a puddle of water that smells of bleach rather than a disinfectant.
How often should the holder itself be cleaned?
Every time you clean the brush. They are one object as far as the smell is concerned.
Elsewhere in the house
Other ELYPRO originals, all patented, all invented because the existing version annoyed us.

Ziplock Bag Dispenser mounts under a cabinet and feeds quart, sandwich and snack bags out one at a time, one-handed. Hardware included. $18.95.

Mug Stackers put a second row of mugs on a shelf that only held one. $24.99 for a six pack, and there is a whole article on how to fit more mugs in a kitchen cabinet if that is the cupboard giving you trouble.