Well, the meaning, which is literal, has something to do with the creation of this world, as per the Holy Qur'an. Even though Qur'an at various places says that the Earth and Heaven were created in six days, the part that mentions Kun Fayakun goes something like 'When He decrees a thing, He says to it only: "Be!" And it is.'
And it seems that as per the holy book that is how this world was created, instantly, with the phrase Kun Fayakun.
Also the song says jab kahin pe kuch nahi bhi nahi tha, vahi tha vahi tha, that is, when there was not even nothing, He alone was there.
This is what I have been able to find with the various resources available at the point. Any suggestions/discussions are welcome.
More from Rockstar:
- Music Review (from Happysing)
- Sadda Haq Aithe Rakh meaning
- Kun Fayakun meaning
- Katiya Karoon meaning
- Phir se Ud Chala: Lyrics, Translation
- Jo Bhi Main: Lyrics, Translation
- Sheher mein: Lyrics, Translation with dialogs
- Aur Ho: Lyrics, Translation
- Tum ko: Lyrics, Translation
- Naadaan Parindey: Lyrics, Translation
- Tum ho: Lyrics, Translation
- Sadda Haq: Lyrics, Translation
For the complete translation of the song, check This Link, courtesy The Bollywood Fan.