S99 may refer to:
*
Avia S-99
The Avia S-199 is a propeller-driven Messerschmitt Bf 109G-based fighter aircraft built after World War II utilizing the Bf 109G airframe and a Junkers Jumo 211F engine in place of the original and unavailable Daimler-Benz DB 605 engine. It is ...
, a Czechoslovak fighter aircraft
* , formerly SAS ''Joanna van der Merwe'', a submarine of the South African Navy
*
Sintura S99, a racing car
* , a submarine of the Soviet Navy
* S99, a
refugee in Nauru
* S99, a
line of the Lucerne S-Bahn
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