The fixtures for the Apertura tournament were announced on 4 July; with the results Real C.D. España 1–0 C.D. Real Sociedad and Atlético Choloma 4–2 C.D.S. Vida, the tournament opened fire on 28 July. On rounds 2 and 3, Vida included midfielder Luis Jaramillo on their lineups despite being ineligible to play; on 12 September, the Northern Disciplinary Commission made the decision to award both matches to Real España and Victoria 3–0. On 28 October, Club Deportivo Olimpia became the first team to secure a spot for the postseason, after defeating Platense F.C. 0–1 at Estadio Excélsior in Puerto Cortés. C.D. Victoria also qualified along Olimpia directly to the semifinals finishing second. On the other hand, C.D. Motagua–Real España and C.D. Marathón–Atlético Choloma had to play a playoff round. The semifinal encounters were settled on 21 November, as Motagua and Atlético Choloma defeated Real España and Marathón respectively. Motagua crushed Real España with a 7–3 on aggregate. Meanwhile, Atlético Choloma dispatched Marathón after a 2–2 aggregated score but with more away goals scored. Once in the semifinals, Olimpia got rid of Atlético Choloma with a 2–1 aggregate, meanwhile Victoria and Motagua finished with a 3–3 global score, however, Victoria advanced thanks to a better regular season finish over Motagua. With their success in the semifinals, Olimpia and Victoria re-encountered each other in a final for the third time in history, having won one each in the previous two. The first match in La Ceiba ended with a scoreless tie; but in the second leg, Olimpia had no mercy over Victoria and won its third consecutive title with an overwhelming 4–0.
Regular season
Standings
Results
Originally Vida 1–0 Real España and Victoria 1–2 Vida. Due to the illegal participation of Vida's midfielder Luis Jaramillo in both matches, Real España and Victoria were granted each a 3–0 win.
Marathón 2–2 Atlético Choloma on aggregate score; Atlético Choloma advanced on away goals.
Semifinals
Olimpia vs Atlético Choloma
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Olimpia won 2–1 on aggregate score.
Victoria vs Motagua
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Victoria 3–3 Motagua on aggregate score. Victoria advanced on better regular season performance.
Final
Olimpia vs Victoria
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Olimpia won 4–0 on aggregate score.
Top goalscorers
10 goals:
8 goals:
7 goals:
5 goals:
4 goals:
3 goals:
2 goals:
1 goal:
1 own goal:
Clausura
The Clausura tournament started on 19 January 2013, the first game was played between locals C.D. Marathón and Platense F.C. at Estadio Yankel Rosenthal. The regular season ended on 20 April 2013. C.D. Olimpia and C.D. Real Sociedad qualified directly to the semifinals after finishing 1st and 2nd respectively. The playoffs were paired with C.D. Victoria facing Deportes Savio and Marathón vs Platense.
Regular season
Standings
Results
Final round
Second round
Victoria vs Deportes Savio
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Victoria won 3–2 on aggregate score.
Marathón vs Platense
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Platense won 4–2 on aggregate score.
Semifinals
Olimpia vs Platense
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Olimpia 0–0 Platense on aggregate score; Olimpia advanced on better regular season performance.
Real Sociedad vs Victoria
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Real Sociedad won 5–2 on aggregate score.
Final
Olimpia vs Real Sociedad
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Olimpia won 2–1 on aggregate score.
Top goalscorers
12 goals:
11 goals:
9 goals:
6 goals:
5 goals:
4 goals:
3 goals:
2 goals:
1 goal:
1 own goal:
Aggregate table
Relegation was determined by the aggregated table of both Apertura and Clausura tournaments. On 20 April 2013, Atlético Choloma was relegated to the Liga de Ascenso after reaching 38 points, two less than C.D.S. Vida.
