AirHint found the following cheapest return flights from Tokyo (NRT) to Kota Kinabalu (BKI) in September 2025 (see full year).

Return flights

16 Sep - 24 Sep	Philippines AirAsia Inc.
29 Sep - 02 Oct	Scoot Tigerair
22 Sep - 26 Sep	Scoot Tigerair
12 Sep - 15 Sep	Philippines AirAsia Inc.
22 Sep - 25 Sep	Scoot Tigerair
26 Sep - 28 Sep	Scoot Tigerair
10 Sep - 24 Sep	Scoot Tigerair
15 Sep - 24 Sep	Scoot Tigerair
09 Sep - 16 Sep	Philippines AirAsia Inc.
12 Sep - 19 Sep	Scoot Tigerair
03 Sep - 07 Sep	Scoot Tigerair
26 Sep - 17 Oct	Jin Air
29 Sep - 17 Oct	Jin Air
25 Sep - 16 Oct	Jin Air
26 Sep - 16 Oct	Jin Air
29 Sep - 16 Oct	Jin Air
29 Sep - 20 Oct	Jin Air

Also check the deals for one-way flights from Tokyo to Kota Kinabalu in September.

The deals are updated regularly. The prices may go up as tickets are purchased by other travellers. Only the cheapest flights are offered. Select a price to book and secure these cheap prices.

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Cheapest return flights from Tokyo to Kota Kinabalu in September from $257

Return flights