The 1999–2000 Kategoria e Dytë was the 53rd season of a second-tier association football league in Albania.
Besëlidhja Lezhë was promoted to the 2000–01 National Championship, with Besa Kavajë had another chance to promotion, playing a tie against 13th-placed team of 1999–2000 National Championship, KF Elbasani.
Besa Kavajë was promoted to the 2000–01 National Championship, with Elbasani being relegated down to the 2000–01 Kategoria e Dytë.
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