Blood from a cut will clot over the wound and cover the exposed nerves sending out pain signals. Splinters are small enough that they don’t trigger bleeding. This means the splinter surface is constantly rubbing against exposed nerves, causing pain. Over time your body will wrap the splinter in a fiber shell to isolate it from the body.
This is also why paper cuts hurt so much. The paper cut is deep enough to expose nerves to signal pain but not deep enough to draw blood and cover the cut.
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