SR 39 begins at SR 1 (Pacific Coast Highway) in Huntington Beach and runs north along Beach Boulevard to Whittier Boulevard in La Habra, with the exception of the segment between the southern city limit of Buena Park and Interstate 5, which was relinquished to the city in 2013.

State maintenance of SR 39 begins again along San Gabriel Canyon Road at the north limit of Azusa.

The highway winds through the San Gabriel Mountains in the Angeles National Forest for 22.6 miles (36.4 km) until it reaches a gate barring the road 0.25 miles (0.40 km) north of Crystal Lake Road in the Crystal Lake Recreation Area.

[11] Although defined to be a continuous route in the California Streets and Highway Code, the segment from Whittier Boulevard in La Habra to West Covina is not officially adopted or signed by Caltrans.

[12] It then continued east with US 60, 70, and 99 to Azusa Avenue where it turned north to follow the present alignment as described beginning in the fourth paragraph of the preceding section.

The new Harbor Boulevard was opened to the public early in 1992, and is now the primary corridor between Orange County and Rowland Heights, although the original winding Fullerton Road segment still exists as a strictly residential street.

During the 1997–98 El Niño event, heavy rainfall caused another rockslide that damaged sections still under construction.

It was predicted that a reopened SR 39 would reduce travel time by around 50% between Mount Waterman and Pasadena, shortening the drive from about two hours to one.

According to Caltrans, work could begin in 2009 on reconstruction, as well as the installation of safety features to prevent future slides from damaging the roadway.

Abandoning the route would not be cost-effective for Caltrans due to, among other reasons, federal environmental restoration requirements related to the presence of bighorn sheep.

[21] The proposal was abandoned after opposition by local residents and the county, as well as substantial legal pressure by the Forest Service, who threatened to enforce an old contract that requires Caltrans to completely deconstruct the highway should it refuse to maintain it.

[21] After lobbying from the cities of Azusa and Glendora, and support from congresswoman Grace Napolitano, Caltrans restarted plans in 2011 toward reopening the closed section of SR 39.

[23] Except where prefixed with a letter, postmiles were measured on the road as it was in 1964, based on the alignment that existed at the time, and do not necessarily reflect current mileage.