How to merge audio and video file in ffmpeg

Merging video and audio, with audio re-encoding

See this example, taken from this blog entry but updated for newer syntax. It should be something to the effect of:

ffmpeg -i video.mp4 -i audio.wav -c:v copy -c:a aac output.mp4

Here, we assume that the video file does not contain any audio stream yet, and that you want to have the same output format (here, MP4) as the input format.

The above command transcodes the audio, since MP4s cannot carry PCM audio streams. You can use any other desired audio codec if you want. See the FFmpeg Wiki: AAC Encoding Guide for more info.

If your audio or video stream is longer, you can add the -shortest option so that ffmpeg will stop encoding once one file ends.

Copying the audio without re-encoding

If your output container can handle (almost) any codec – like MKV – then you can simply copy both audio and video streams:

ffmpeg -i video.mp4 -i audio.wav -c copy output.mkv

Replacing audio stream

If your input video already contains audio, and you want to replace it, you need to tell ffmpeg which audio stream to take:

ffmpeg -i video.mp4 -i audio.wav -c:v copy -c:a aac -map 0:v:0 -map 1:a:0 output.mp4

The -map option makes ffmpeg only use the first video stream from the first input and the first audio stream from the second input for the output file.

Since I am not allowed to write comments to the first answer with my reputation, an addendum here, because I had this problem when encoding webms.
If your audio stream is for example longer than the video stream, you have to cut it or otherwise you will have the last video frame as a still image and audio running.

To cut either stream, you can use -ss [hh:mm:ss] -t [ss] before each of the -i "file.ext".
-ss [...] will define the starting point to cut
-t [...] will define the length of the segment in seconds

Example:

ffmpeg.exe -ss 00:00:10  -t 5 -i "video.mp4" -ss 0:00:01 -t 5 -i "music.m4a" -map 0:v:0 -map 1:a:0 -y out.mp4

Open command promt (windows+R -> Cmd+Enter). Then go to inside the folder where you have audio and video file. Apply this command:

ffmpeg -i "videoFile.mp4" -i "audioFile.mp3" -shortest outPutFile.mp4

You will get a new file named outPutFile.mp4 (a merged file of audio and video)