If you’re having a tough time with the last (smallest) one or two gears clicking when you shift to them, you’re probably also having a tough time getting the shifting dialed in for the rear derailleur overall. The barrel adjuster has to be set precisely or that last gear or two will click as you pedal with the bike on the stand.
Now, there are a few reasons for gears “clicking” or skipping, so the cause of the others have to be eliminated first because this last tip is on the drastic side.
Have you tried dialing in the rear derailleur properly? If you just can’t get it right so all of the gears are quiet, read on. Is there drag in the system? The rear derailleur can be a little finicky because you’ve got a long cable traveling through a lot of housing to get to that derailleur. If there’s any drag in that cable, if it can’t move freely because of so much as a blob of mud splashed in the wrong place, you will have gears that skip and you’ll never be able to get the shifting quite right with the barrel adjuster (in this case, your chain won’t just skip, it’ll jump). Is your rear derailleur in proper working order? Clean and lube the joints and jockey wheels. Speaking of the jockey wheels, are they moving freely? Take the chain off completely to check they are (this is a common problem and an easy thing to miss – nobody checks the jockey wheels). And all of this assumes your chain and cassette are at the beginning half of their useful life…
Now, if you can check each of those off and you’re still skipping in the two smallest gears on the cassette, you’ve likely recently done one of two things; changed the chain line or installed a new rear derailleur. Or your new bike was came straight from the shop “a little off” (I had this happen to one of my bikes, so I included it – this one is rare). In this case, the likely culprit is your limit screws are just a bit off. If it’s the smallest or the two smallest gears, it’s the low limit adjuster screw. If you can’t quite get into the big gear in the back, it’s the high limit screw.
When you go to fix this, using Shimano’s derailleurs as my example, the set screws are a little kittywampus. If you’re looking at the derailleur from the back of the bike, the one on the right handles the big cog and the one on the left handles the little cog.
We’re going to check one thing first, and this is absolutely urgent – especially for us cool kids who take the plastic spoke protector off seconds after we get the bike home… with the bike in a stand or flipped upside down on the floor in front of you, shift to the smallest cog in the back. Then, pedal the bike and manually operate the rear derailleur so it shifts all the way to the big gear. Now, stop pedaling when the chain gets to the big cog, because we’re going to try to overshift it which would drop the chain into the spokes [!]. Dropping the chain into the spokes from the cassette with the wheel moving is all bad. If we do this while we’re pedaling and the chain gets caught, you’re going to damage spokes, possibly the chain, and all kinds of really, really bad things are going to happen, up to and including a pooched wheel and bent hub, so be careful.
Without pedaling, if you can push on the derailleur so the jockey wheel and the chain pass the biggest gear toward the spokes, stop everything immediately. We have to set the high limit screw (the one on the right). You want your jockey wheel to line up exactly with that big gear, in the same line, and you should be able to push pretty hard on that derailleur arm and the closest jockey wheel shouldn’t move a hair beyond that imaginary line, plumb with the center of that big cog. To move the jockey wheel right (away from the spokes) turn the set screw on the right counterclockwise. To move the jockey wheel left (toward the spokes) turn the set screw on the right clockwise.
With the big gear set perfectly, now we’re going to look at the small. With pressure on the derailleur arm to keep the chain on the biggest cog, start pedaling again and manually operate the derailleur so the chain drops to the small cog. Now, you created a massive amount of slack in the shifter cable by operating the derailleur to the big cog without shifting. You have to make sure the cable and the housings are seated properly in the stops when you let the derailleur work back to the small cog. Check that, and we can move on.
For the pulley wheel at the small cog, we don’t want the pulley wheel directly lined up with the small cog (like we did with the big cog). We want the jockey wheel just outboard of the smallest gear – just to the right of that imaginary plumb line below the smallest cog if you’re looking at the derailleur from the back. You’re likely currently set so that pulley wheel is just under, or even inboard of that small gear (toward the next cog up). That’s why you’re skipping in the last gear or two and can’t quite get it set right with the barrel adjuster – the limit screw is stopping the derailleur from properly engaging that last gear (or two). Again, looking at the derailleur from the back, turn the set screw on the left counterclockwise to move the pulley wheel outboard (to your right) so that the center of the jockey wheel is to the outside edge of that smallest cog.
Now your rear derailleur is set properly.
Set your cable tension with the barrel adjuster so you get smooth shifts up and down the cassette and Bob’s your uncle.
As a final note, it’s exceedingly rare to have to adjust the set screws. One should undertake this as a last resort only, after all other options (including new cable housings all the way to the derailleur) are exhausted. If the screws were set properly in the first place, you don’t ever have to touch them unless you change the chain line (new derailleur, add a shim behind the cassette, etc.) you will open up a can of worms that you’ll find is hard to put the lid back on.