This term is difficult to define, as it is just that: the fundamental frequency. If you play a certain note on an instrument, the instrument will produce the frequency of the note, but also other frequencies (overtones and undertones).
The fundamental frequency is the frequency of the note being played and is the most pronounced frequency in the instrument or vocal sound.
For example, the frequency of the note A on the third string, second fret of your guitar is about 440 Hz (depending on tuning). If you play this A the fundamental frequency of the sound produced by the guitar is about 440 Hz, but the guitar, due to its construction, will produce other frequencies as well.