| 1 | Shyan VaziriPlace 1 · Scripps Ranc | — | Scripps Ranc | 4:13.23 |
| 2 | Trent WarrenPlace 2 · Eastlake | — | Eastlake | 4:19.98 |
| 3 | Jack WilsonPlace 3 · Cathedral Ca | — | Cathedral Ca | 4:20.75 |
| 4 | Brad LittooyPlace 4 · Scripps Ranc | — | Scripps Ranc | 4:21.67 |
| 5 | Darren FahyPlace 5 · La Costa Can | — | La Costa Can | 4:22.59 |
| 6 | Ryan SchallPlace 6 · Westview | — | Westview | 4:22.82 |
| 7 | Eric CauseyPlace 7 · La Costa Can | — | La Costa Can | 4:23.13 |
| 8 | Scott GiselPlace 8 · Rancho Buena | — | Rancho Buena | 4:25.23 |
| 9 | Connor TorrePlace 9 · Madison | — | Madison | 4:25.75 |
| 10 | Andrew RichardsonPlace 10 · Carlsbad | — | Carlsbad | 4:29.11 |
| 11 | Angel SaucedaPlace 11 · Point Loma | — | Point Loma | 4:31.43 |
| 12 | Nicasio WestlundPlace 12 · Valley Cente | — | Valley Cente | 4:34.74 |
| 1 | Emmanuel CorveraPlace 1 · Serra | — | Serra | 4:40.81 |
| 2 | Mickel EsquivelPlace 2 · University | — | University | 4:42.78 |
| 3 | Cory LozanoPlace 3 · Serra | — | Serra | 4:44.26 |
| 4 | Matthew DumesnilPlace 4 · Point Loma | — | Point Loma | 4:46.68 |
| 5 | Nathan JumpsPlace 5 · University | — | University | 4:51.46 |
| 6 | Sergio GonzalezPlace 6 · Mt Miguel | — | Mt Miguel | 4:51.55 |
| 7 | Gabriel MaganaPlace 7 · Castle Park | — | Castle Park | 4:55.13 |
| 8 | Stephen LopezPlace 8 · Valley Cente | — | Valley Cente | 4:57.81 |
| 9 | Rodrigo ParedesPlace 9 · Castle Park | — | Castle Park | 4:58.45 |
| 10 | Isidoro RendonPlace 10 · University | — | University | 5:00.55 |
| 11 | Abel LagunasPlace 11 · Hoover | — | Hoover | 5:01.96 |
| 12 | Jose HernandezPlace 12 · Madison | — | Madison | 5:02.14 |
| 13 | Mason SmithPlace 13 · Mountain Emp | — | Mountain Emp | 5:02.15 |
| 14 | Leo GomezPlace 14 · Mt Miguel | — | Mt Miguel | 5:05.29 |
| 15 | Antonio SandovalPlace 15 · Castle Park | — | Castle Park | 5:09.86 |
| 16 | Mulugeta EndgawPlace 16 · Hoover | — | Hoover | 5:15.11 |
| 17 | Eric BergPlace 17 · Calvin Chris | — | Calvin Chris | 5:17.05 |
| 18 | Cesar LopezPlace 18 · Castle Park | — | Castle Park | 5:19.74 |
| 19 | Justin KirkPlace 19 · Madison | — | Madison | 5:19.94 |
| 20 | Brian EscalantePlace 20 · Castle Park | — | Castle Park | 5:29.48 |
| 21 | Patrick PattonPlace 21 · Mountain Emp | — | Mountain Emp | 5:48.27 |
| 1 | Kyle LynchPlace 1 · Rancho Buena | — | Rancho Buena | 4:26.42 |
| 2 | Eric MunozPlace 2 · Escondido | — | Escondido | 4:28.93 |
| 3 | Nick BieragelPlace 3 · Mission Hill | — | Mission Hill | 4:28.98 |
| 4 | Enrique RiveraPlace 4 · Fallbrook | — | Fallbrook | 4:29.94 |
| 5 | Omar RomeroPlace 5 · Escondido | — | Escondido | 4:31.32 |
| 6 | Zach VelasquezPlace 6 · Otay Ranch | — | Otay Ranch | 4:35.09 |
| 7 | Jared SenesePlace 7 · Mt Carmel | — | Mt Carmel | 4:35.74 |
| 8 | Taylor RobinsonPlace 8 · Steele Canyo | — | Steele Canyo | 4:36.90 |
| 9 | Derek StotlerPlace 9 · Rancho Buena | — | Rancho Buena | 4:38.52 |
| 10 | Aaron WestonPlace 10 · Steele Canyo | — | Steele Canyo | 4:40.16 |
| 11 | Richard MartinezPlace 11 · Otay Ranch | — | Otay Ranch | 4:41.06 |
| 12 | Max LatifiPlace 12 · Mt Carmel | — | Mt Carmel | 4:42.46 |
| 13 | Andrew Toedt-WileyPlace 13 · Steele Canyo | — | Steele Canyo | 4:44.52 |
| 14 | Carlos RangelPlace 14 · Otay Ranch | — | Otay Ranch | 4:45.18 |
| 15 | Kevin ChenPlace 15 · Westview | — | Westview | 4:47.66 |
| 16 | Angel JaimesPlace 16 · El Camino | — | El Camino | 4:49.51 |
| 17 | Dalton CasePlace 17 · Cathedral Ca | — | Cathedral Ca | 4:50.28 |
| 18 | Tyler TonyPlace 18 · San Pasqual | — | San Pasqual | 4:50.49 |
| 19 | Jason HaysPlace 19 · Otay Ranch | — | Otay Ranch | 4:53.66 |
| 20 | Allan PansegrauPlace 20 · San Pasqual | — | San Pasqual | 4:55.34 |
| 21 | Christopher JohnstonPlace 21 · El Camino | — | El Camino | 4:56.45 |
| 22 | Joel KosmatkaPlace 22 · Cathedral Ca | — | Cathedral Ca | 4:56.76 |
| 23 | Teague SenningerPlace 23 · Granite Hill | — | Granite Hill | 4:57.01 |
| 24 | Dominic LucisanoPlace 24 · Westview | — | Westview | 4:59.01 |
| 25 | Alex GarciaPlace 25 · Steele Canyo | — | Steele Canyo | 4:59.80 |
| 26 | Nick IsrealPlace 26 · Mission Hill | — | Mission Hill | 5:12.63 |
| 27 | Jonny WalkerPlace 27 · Granite Hill | — | Granite Hill | 5:20.75 |