The 2003 season was Cienciano's season since its founding in 1901. The club participated in the 2003 Torneo Descentralizado and 2003 Copa Sudamericana. This season was one of the most successful seasons for Cienciano as they won the 2003 Copa Sudamericana, the first and only international title for a Peruvian club.
| Club: | Cienciano |
| Season: | 2003 |
| Manager: | Édgar Ospina (until May) Freddy Ternero |
| Chairman: | Juvenal Silva |
| League: | Torneo Descentralizado |
| League Result: | Full Table: 7th *Apertura: 4° *Clausura: 8° |
| Cup1 Result: | Champion |
| Pattern La1: | _whiteborder |
| Pattern B1: | _collarwhite |
| Pattern Ra1: | _whiteborder |
| Pattern Sh1: | _red stripes |
| Pattern So1: | _socks |
| Leftarm1: | FF0000 |
| Body1: | FF0000 |
| Rightarm1: | FF0000 |
| Shorts1: | FFFFFF |
| Socks1: | FF0000 |
| Prevseason: | 2002 |
| Nextseason: | 2004 |
Last updated in January 2003.|}
| Date | Opponents | H / A | Result F - A | Scorers | Attendance | |
|---|---|---|---|---|---|---|
| 7 Aug. 2003 |  Alianza Lima | H | 1 - 0 | Martín Raúl García 9' | ||
| 26 Ayg. 2003 | Alianza Lima | A | 0 - 1 | Roberto Holsen 22' | ||
| 25 Sep. 2003 | Universidad Católica | H | 4 - 0 | Carty 1', Cristian Álvarez (o.g.) 38', Acasiete 55', Paolo Maldonado 69' | ||
| 2 Oct. 2003 | Universidad Católica | A | 1 - 3 | Cristian Álvarez (o.g.) 9' |
| Date | Opponents | H / A | Result F - A | Scorers | Attendance | |
|---|---|---|---|---|---|---|
| 16 Oct. 2003 |  Santos FC | A | 1 - 1 | Alex (o.g.) 71' | ||
| 29 Oct. 2003 | Santos FC | H | 2 - 1 | Carty 11', 34' |
| Date | Opponents | H / A | Result F - A | Scorers | Attendance | |
|---|---|---|---|---|---|---|
| 13 Nov. 2003 |  Atlético Nacional | A | 2 - 1 | Carty 29', Paolo Maldonado 84' | ||
| 4 Dec. 2003 | Atlético Nacional | H | 1 - 0 | Carty 1' |
| Date | Opponents | H / A | Result F - A | Scorers | Attendance | |
|---|---|---|---|---|---|---|
| 10 Dec. 2003 |  Club Atlético River Plate | A | 3–3[1] | Portilla 26', 79' Carty 67' | ||
| 19 Dec. 2003 | Club Atlético River Plate | H | 1–0[2] | Lugo 78' |
| 3 | Coronel Bolognesi | 22 | 9 | 8 | 5 | 30 | 22 | +8 | 35 | ||
| 4 | Cienciano | 22 | 10 | 4 | 8 | 31 | 22 | +9 | 34 | 2003 Copa Sudamericana qualifying round | |
| 5 | Sport Boys | 22 | 8 | 7 | 7 | 34 | 28 | +6 | 31 |
Copa Sudamericana 2003 qualifying
| Pos | Team | Pld | W | D | L | GF | GA | GD | Pts | |
|---|---|---|---|---|---|---|---|---|---|---|
| 7 | Unión Huaral | 15 | 6 | 3 | 6 | 12 | 17 | −5 | 21 | |
| 8 | Cienciano | 14 | 4 | 3 | 7 | 17 | 20 | −3 | 15 | |
| 9 | Atlético Universidad | 14 | 4 | 3 | 7 | 10 | 18 | −8 | 15 |