[9] While at the Electronic Frontier Foundation, Eckersley started projects including Let's Encrypt, Privacy Badger, Certbot, HTTPS Everywhere, SSL Observatory and Panopticlick.

There, he started working for the Electronic Frontier Foundation and set up a sharehouse, where he lived with roommates including computer scientist and activist Aaron Swartz.

[13][14] From 2006 to 2018, Eckersley worked at the Electronic Frontier Foundation (EFF) in roles including technology projects director, chief computer scientist, and head of AI policy.

In 2007, Eckersley and other collaborators conducted a controlled experiment to prove that the Comcast telecommunications company tampered with peer-to-peer protocols such as BitTorrent through the use of forged reset packets.

[17] His later work in this field resulted in the Panopticlick, an EFF website to test the identifiability of users' web browsers, as well as advocacy for stronger enforcement of the Do Not Track header.

[18] He collaborated in that work with Aaron Swartz, another online privacy advocate with close ties to the Electronic Frontier Foundation.

[21] Many other web-scale services for securing sites have built on the certificate infrastructure provided by Let's Encrypt, including Certbot, Caddy, and Traefik.

[1][26] He was remembered by the Wall Street Journal as an "Australian computer scientist," who "worked at a San Francisco nonprofit on projects designed to protect privacy.