The Hong Kong National Security Law was passed by China's Standing Committee of the National People's Congress on 30 June 2020 and took effect the same day. Its provisions — criminalising secession, subversion, terrorism, and collusion with foreign forces — carried penalties up to life imprisonment and applied without the procedural constraints of Hong Kong's existing legal system. Chow had been a prominent member of Demosistō, the pro-democracy political party co-founded by Joshua Wong. On the day the law passed, she announced her withdrawal from the organisation on social media. She said she would no longer participate in international advocacy work and would not accept foreign media interviews. She described it as a decision made in the new reality the law had created.

Police arrested nine people that night, including Jimmy Lai, founder of Next Digital and publisher of the Apple Daily newspaper. Then officers arrived at Chow's residence. Her lawyer was present. She was taken in. Senior Superintendent Li Kwai-wah of the National Security Department told reporters that ten people in total — nine men and one woman, ranging in age from 23 to 72 — had been arrested on suspicion of colluding with foreign forces and conspiracy to commit fraud. A search warrant issued four days earlier, on 6 August, authorised the search of Chow's home. Police seized her computer, mobile phone, and campaign materials. She was held at Tai Po Police Station. After more than 24 hours in custody, she was released on bail of HK$200,000, with a surety of HK$180,000. Her Hong Kong SAR passport was confiscated. She was ordered to report back to police on 1 September.

When Chow emerged from Tai Po Police Station, reporters were waiting, along with fellow activists Joshua Wong and Tiffany Yuen. She called the arrest the most frightening experience of her life — not because of what had happened to her in custody, but because of what she understood the law to mean: that if charged under it, she would likely not receive bail. In detention, she had found comfort in a song by the Japanese group Keyakizaka46, "Fukyouwaon." Released, she immediately broadcast live in Cantonese and Japanese, explaining what had happened and urging people — particularly in Japan, where she had a substantial following — to pay attention to what was unfolding in Hong Kong. She learned during her detention that the Apple Daily had printed 550,000 copies that day, far above its usual run. That detail, she said, mattered to her.

The reaction in Japan was immediate and substantial. Major news organisations ran the arrest as breaking news. On Twitter, hashtags including #FreeAgnes and #周庭氏の逮捕に抗議する — "Protesting the arrest of Agnes Chow" — trended widely. Japan's Chief Cabinet Secretary Yoshihide Suga expressed deep concern. A cross-party parliamentary group held an emergency press conference. The French news weekly Le Point put Chow and Joshua Wong on its cover on 20 August, under the headline Les derniers jours de Hong Kong — "The Last Days of Hong Kong." In Taiwan, the youth wing of the ruling Democratic Progressive Party described the arrest as evidence that Beijing's promise of "one country, two systems" was no longer operative. From across the region and further, the arrest of a 23-year-old activist had become a signal event about what Hong Kong was becoming.

On 1 September, Chow reported to Tai Po Police Station as required. Police asked her to return on 2 December. She hoped, she said, to spend her birthday in freedom. She did not. On 2 December 2020, Chow was sentenced to prison on separate unlawful assembly charges — an outcome that meant she could not report to the station as required, because she was in custody. She was released in 2021 and continued to comply with bail conditions for the National Security Law case, reporting periodically and quietly, without press present. The charge of inciting secession under the National Security Law continued to hang over her. In December 2023, Agnes Chow announced from Canada that she would not return to Hong Kong. She was 26.