Tu Kuja Man Kuja is Persian, that is Farsi, for the next line, Tu kahaan, main kahaan. Tu is tu, you. Man is main, I. And Kuja is kahaan, where.
Hence, Tu Kuja man kuja means 'where are you, where am I', or 'tu kahaan, main kahaan' as Sunidhi sings in Hindi.
One interesting thing is that except for this one line, the entire song is Hindi, to a large extent filled with quite Sanskrit-like (known as tatsam) words, making it a meeting of extremes, as Urdu and Hindi are almost derived from Persian and Sanskrit which are older, more pure languages, and while Urdu and Hindi go hand in hand, Persian and Sanskrit are hardly ever used together.
[For the complete Highway song, see THIS POST.]