How to set the intonation on a Strat

Do it yourself — fresh strings and a tuner are all you need. ezietsman, our Amp Whisperer, says there's no need for a tech: the bridge saddles on a Strat are easy to adjust yourself ⁶.

Check first

Tune the open string with a good tuner, then compare the fretted 12th fret note to the 12th fret harmonic. If they differ, that string's intonation is out ³, ⁶.
Use fresh strings — this is essential; old strings give false readings ⁶.

The adjustment

Sharp at the 12th? Move the saddle back, away from the nut, to lengthen the string ², ⁸.
Flat at the 12th? Move it towards the nut.
Loosen the string first, turn the saddle screw with a screwdriver, retune and re-check. Repeat string by string ⁸.
Be realistic — within about 3 cents is fine; almost nobody hears less than that ¹. On the G and B strings aim spot-on or slightly flat, never sharp ¹.

If low frets are still sharp

Suspect the nut or action. If open chords sound out even when the 12th is spot on, the nut is likely too high or the action too high — fretting stretches the string sharp. Nut work needs files and a steady hand, so leave that to a pro ³, ⁵, ⁶.
Check relief first. Order of operations: truss rod, then action, then intonation ⁸.

Full step-by-step with photos in our own setup guide: check thread ².

From these forum threads

Setting Intonation (2008): How accurate is accurate? Alan's cents-tolerance for intonation
Guitar Maintenance 5 – Setting Intonation (2010): Alan's full intonation guide with theory and checking method
Guitar tuning and intonation (2010): Simple 12th-fret test to tell tuning from intonation
Intonation Issues (2016): When sharp notes everywhere mean a nut problem, not saddles
attention guitar tech's who know fenders, intonation prob with brand new guitar (2011): Why the 12th-fret harmonic check is the one that counts
How easy is it to do your own setup? (2007): DIY setup order: truss rod, action, then intonation