If the strings are old, rusty or at all manky: replace them. Makes a real big difference when setting the intonation. Old strings can be impossible to bring into tune - and naturally the intonation would be out when you replaced them anyhow.
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If that doesn't work look down the neck to see if its straight. You might have to adjust the truss rod.
If it's flat, you need to shorten the string. Move the saddle in toward the nut, not farther away.
12th Fret Plays Sharp: move the saddle away from the nut
12th Fret Plays Flat: move the saddle closer to the nut
(Don't try to do it by ear. Use a tuner, if you have one.)