He returned to his private practice in San Francisco from 1980 to 1998 with Morrison & Foerster, when he briefly served as a special counsel in the Antitrust Division of the Department of Justice in 1998.

Regarding the removal of people incorrectly included in the list, he ruled that, "[t]he government's administrative remedies fall short of such relief and do not supply sufficient due process.

[14] In September 2017, Judge Alsup was assigned four cases by parties suing to halt President Trump's decision to end the Deferred Action for Childhood Arrivals program created by Barack Obama.

[17] On July 27, 2018, Judge Alsup dismissed a lawsuit targeting ExxonMobil on the basis that two California cities, San Francisco and Oakland, could not prove the energy company was responsible for climate change in the state.

Alsup's ruling was based on borrower defense, which allows students to have their loans forgiven if the university lies to them about their job prospects, credit transferability or likely salary after graduation.