The 2003 Esiliiga is the 13th season of the Esiliiga, second-highest Estonian league for association football clubs, since its establishment in 1992.
FC Valga beat JK Tervis Pärnu 5–2 on aggregate. Vaga stayed in Meistriliiga, Tervis in Esiliiga.
FC TVMK II Tallinn beat FC Merkuur Tartu 6–2 on aggregate. TVMK II promoted to Esiliiga, Merkuur relegated to Second Division.