The site, called Playpen, was located on the Tor network used to anonymise web-browsing activity.
Fluckiger was "heavily involved" in the running of the members-only site, said the US Department of Justice (DoJ).
The investigation into the site has led to the rescue of 49 American children who had been subject to abuse.
Fluckiger of Portland, Indiana, was "co-administrator" of the site, said the DoJ, and helped Playpen members see and read "tens of thousands" of messages relating to the sexual abuse of children.
He managed membership lists, enforced site rules and deleted any content that was not related to indecent images of children.
Two other men who helped run the site, David Lynn Browning of Kentucky and Steven W. Chase of Florida, have pleaded guilty and are due to be sentenced soon.
Across the US, 48 active child abusers have been prosecuted as a result of the investigation, said the DoJ. It added that, in total, 200 prosecutions had resulted from the long-running investigation.
Playpen was located on a server on the well-known Tor network which hides the identity and location of browsers by encrypting data and bouncing it between different computers.
Law enforcement agencies caught the site administrators, and many members of Playpen, by using techniques that stripped them of the anonymity Tor can provide. Legal challenges against this investigative technique have been filed by some alleged Playpen members.
Once the site's administrators had been arrested, the FBI kept the site going for 13 days to gather information about members.
American Michael Fluckiger has been sentenced to 20 years in jail for running a site that trafficked images of child sex abuse.