Fuelly calculations not matching car's
 

I have a 2008 Prius, bought second-hand here in Japan a few years ago. I get pretty good mileage (kilometerage?) according to the car's calculations (between 22-25 km/l) but when I enter the car and gas-pump figures into Fuelly, Fuelly reports significantly lower rates, between 1 and 2 km/L lower. I can do the calculations by hand and the figures match what I expect, so I'm wondering how Fuelly calculates its mileage. I was told by the previous owner that the car has bigger tires (19"?) than the standard Prius (__?) and that those bigger tires actually lower the mileage. Fuelly doesn't seem to account for tire size, so this discrepancy in Fuelly is even more puzzling. Any ideas?

Welcome. Check your Settings in Fuelly. Make sure you have chosen the correct values you want to work in.
When you input the data, input the litres and total cost and let Fuelly calculate the cost per litre or litres and cost per litre and let Fuelly calculate the total cost. If you input total cost and cost per litre then errors on rounding up and down can throw your litre value off. The most important numbers are the litres and miles (or kilometres) for working out your fuel efficiency.
I use three different systems (Fuelly, SpiritMonitor and my own spreadsheet) and always get three slightly different answers.

This should tell you the difference between the tire sizes.
https://tiresize.com/calculator/

Even without the different tires, Toyota's display is optimistic when it comes to fuel consumption. My Camry's lifetime is at least 2mpg more than Fuelly's.

I hadn't noticed the original post was referring to the onboard computer against Fuelly. I thought it was comparing a calculated figure against Fuelly. The onboard computer just plucks a number out of the ether, for all the good it does.

They're not all that bad, mine isn't the best, about 92% accurate, but the one in my Honda was extremely close to the actual numbers.

Over a full tank's worth, the one on my Honda is normally within 2%. The trouble is, it can be 2% high one time and 2% low the next, though normally it is optimistic.

If the tires you have are a overall larger diameter than what the odometer is calibrated for, you will be driving more kilometers than what the vehicle's odometer states (larger diameter = more distance traveled per axle revolution). Likewise, if the tires have a smaller diameter, you will drive fewer miles than what the odometer states.

However, changing to a "larger" tire doesn't necessarily mean the overall diameter of the tire is any different than the previous "smaller" diameter tire. The tire size is measured by the inside diameter (i.e., the diameter of the wheel), not the outside diameter of the tire (from tread to tread).

The vehicle's computer can be be changed to calculate mileage more in line with actual fuel useage.

As mentioned, changing tire size throws the odometer off which throws the optimismeter off. Those tires almost assuredly reduce fuel mileage as well. I've never understood why anyone would buy a hybrid which is all about mpg and then do something to it to reduce mpg.

I'm thinking about going to a smaller, narrower but taller tire that will be less than 1% different diameter to my originals so my speedometer/odometer will be fine but it will take 68 pounds of unsprung weight away and be a smaller "wall" of tire to push through the air as I drive.