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ffmpeg -i track1.wav -ss 00:00:38.160 -t 00:00:20.720 -vn -codec:a libmp3lame -ac 2 -b:a 256k -map a -af afade=t=in:ss=38:d=3,afade=t=out:st=55:d=3 output.mp3

This is how I am cutting the audio file. My problem is, Fade in not working and fadeout working very well. But if I cut audio from the beginning (0:0), Fade in and fade out working perfectly.

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Your command is wrong, use this one: ffmpeg -i track1.wav -ss 00:00:38.160 -t 00:00:20.720 -vn -codec:a libmp3lame -ac 2 -b:a 256k -map a -af afade=t=in:st=38:d=3,afade=t=out:st=55:d=3 output.mp3

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    I had read you answer 3 times to see the one letter of the difference. It would by nice to include it in your answer, and explain the reason for it. – MarianD Jun 8 '19 at 5:45

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