Why does my Nikon D5300 overexpose compared with my D40, even at the same settings?

Have you checked the aperture stop down lever on the D5300 to see if it looks bent?

If it is, your lens may not be stopping down as much as the camera thinks it is. This is a fairly well known and common problem. If a lens is not properly aligned when twisted on to mount, it can damage the lever. This almost always results in overexposure.

Most current camera systems use an electronic connection between the camera and lens to control the aperture diaphragm. Nikon has only recently started making a few lenses with what they call electromagnetic diaphragms and only fairly recent Nikon bodies can control them. The vast majority of lenses produced since the 1950s in the Nikon F-mount system use the less elegant mechanical linkage to control the aperture.

The blue arrow points to the camera's aperture control lever.

You can test it by using your lens with the widest maximum aperture (lowest f-number). Start with the aperture set manually to wide open, look into the front of the lens, and either press the depth of field preview button or set the camera to "Bulb" exposure and hold the shutter button all the way down. You might need to turn off auto focus to get the camera to activate the shutter without achieving focus first.

Notice the position of the aperture diaphragm. Then progressively stop down the lens one click at a time (1/3 stops, 1/2 stops, or whole stops depending on your lens and also your camera settings with some newer types of Nikon F-mount lenses).

Does the aperture stop down a little more for every increase in the f-number setting? If it doesn't start moving any more than when it is wide open when set to the first few settings that are slightly narrower than wide open, that indicates your aperture lever is in need of adjustment.

Another possibility: If you have "Active D-lighting" enabled, turn it off and see if that solves your issue.

If the actual ISO, exposure time, and aperture value are the same, one camera should not produce significantly brighter pictures than the other.

Exposure compensation should make no difference if the actual ISO, Tv, and Av used for both cameras are the same. Neither should differences in metering.

Beyond the above:

Though it may seem significant to you, there's really not that much difference between the two cameras.

Back in the heyday of film, it was not unusual to get two batches of the same film that varied by that much. That's why the perfectionists would buy a whole brick of film at a time and run a density test on one roll to establish how much it varied from the rated box speed.

The mechanical linkage that is used to control most F-mount lenses is notorious for minor inconsistency from shot to shot. But it doesn't end there. Like all mechanical devices with moving parts and wear surfaces, continued usage will cause minor changes in how far the aperture is stopped down. They need to be periodically checked and adjusted back to factory specs.

It may well be that when your D40 was new it stopped down each lens slightly less and exposed brighter than it does now after it has been used for several years. It may also well be that when you've used the D5300 for that many clicks, it will also stop down the lens slightly more than it does now.

It also may well be that Nikon just decided to make the processed images from the same exposure levels slightly brighter for the D5300 than the D40.

There's no absolute "perfection" when it comes to exposure, f-stops, shutter times, and ISO/film sensitivity. In the purely mechanical camera era with film, anywhere within one-sixth stop was considered "spot on".

For more, please see:

Is there a sane reason why ¹⁄₁₂₅ is not, instead, exactly half of ¹⁄₆₀?

Why are these film photos brighter than digital photos taken at the same time with the same settings? (Each of the answers looks at different aspects that contribute to the difference in final result of images taken with the same settings with two different cameras, one film and one digital.)

This answer to Am I wrong to judge my exposure using my smartphone?