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In designing a linear power supply, I understand I need to limit the inrush surge current on cold start, to charge up the large bank of filter capacitors, post-rectifier.

However, my original intent was to connect the transformer directly to the power entry module/fuse/breaker without a PC board in the path. Only the secondary stepped-down side would have a PC board and therefore could accommodate a thermistor.

Does it matter whether the NTC Thermistor for inrush current limiting is connected to the primary mains voltage or secondary winding of the transformer [before rectifiers]? My initial intuition is no, since they are proportional in current anyways, and limiting one winding will naturally limit the other.

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A transformer can have many times the normal current on startup as it is unlikely that it get turned on at zero crossing. Depending on the actual rating of the transformer, this might not be an issue.

So the general answer to your question is, yes, it does make a difference what side of the transformer you put the Thermistor

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