The airport operates from a single terminal that handles both arrivals and departures. Passenger processing areas - check‑in, security and the departure lounge - are contained within a compact building. The terminal supports domestic operations and limited international services on certain routes.

The airport is a short drive from Kupang city center; taxis and private cars are the main transfer options.

• Rail/metro: None.
• Buses: Local buses and minibuses serve nearby routes but may not call at the terminal directly.
• Taxis: Taxis provide reliable transfers to central Kupang; agree a fare or use an app if available.
• Ride‑share: App services may be limited; rely on local taxis.
• Driving: Accessible by road with parking available on site.

Facilities are focused on regional passenger needs.

• Lounges: Large airline lounges are uncommon.
• Food & drink: Small cafés or kiosks are usually available landside.
• Wi‑Fi: Public Wi‑Fi availability varies.
• Charging stations: Limited - bring a portable charger.
• Luggage storage & showers: Not typically available.
• Accessibility: Assistance can usually be arranged through airlines.

Hotels are concentrated in Kupang city; there is no major on‑site airport hotel. Travelers typically book accommodation in the city and use a taxi for the short transfer to El Tari Airport. For overnight or long layovers, city hotels are the practical choice and many offer airport pickups on request.