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I'm just starting out on the ukulele coming from a guitar background. Compared to the guitar, the intonation isn't great, and from everything I've read, the shorter neck means that's the nature of the instrument.

The uke is new, from one of the K brands, and professionally set up.

I'm not sure if I should tune it so the open string is in-tune, a fretted string, or compromise (and if I do, which which fret)?

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It all depends on what you will be playing but it'd be wise to compromise and tune to your median fret. I know that if I am going to be playing around the 10th fret then I'll tune my guitar to the 10th fret.

This technique won't be practical when playing in all ranges of frets. You can however sharp/flattern a string to best compensate with what you'll be playing but sometimes finding that compensation point doesn't help your situation at all and can make both ranges of frets sound out of tune.

A good way to fight this is to be more tactical in your playing and instead of jumping up to the 8th fret for a note, just simply play the same note on another string that brings it into the lowFret->higherFret fret range - the range of where it would be 'safe to play' without having noticeably bad intonation issues on your ukulele.

Hope this helps :)

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  • This led me down an interesting rabbit hole on equal temperament and guitars with frets at different locations for each note so every note is in tune. I also got to read up on the other temperaments and how the equal temperament is a compromise between integer ratios for intervals and being able to transpose a piece into another key.
    – David Ehrmann
    Jan 16, 2017 at 0:17
  • @DavidEhrmann- this is indeed a rabbit hole. Theoretically, you really need moveable frets to get perfect intonation, even equal temperament, on the guitar, because of having strings of the same material, but different pitches at the same length. If you want a look at what can be done with such a guitar, with frets tuned to "funny" temperaments, check out the wonderful music of tolgahan çoğulu- youtube.com/watch?v=MYK_PF9WTRE
    – Scott Wallace
    Jan 18, 2017 at 19:26
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While you can retune so that more of what you're playing will be in tune, I think it's better to fix the problem. Ukes can have good intonation with a proper setup. I find that the best solution to intonation issues up the neck is to cut a compensated saddle for the uke. It's not perfect but it's the best solution I've found.

The general procedure is to measure the amount of deviation from the norm and compensate for it. On each string, find out how sharp or flat the note at the 12th fret is. When you get those numbers, the next step is to file a saddle so that the point of string contact makes the string slightly longer or shorter than the others. It's more or less a manual version of setting the intonation on an electric guitar with individual saddles.

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