Media reports suggest that anywhere between 500 to several thousand people gathered in Ljubljana's Kongresni trg square, from where the group marched to the National Assembly and on to the US Embassy.
In Maribor a smaller group of about 100 people protested at the Leon Štrukelj Square.
Gregor Plemenka, one of the initiators of the rally in Ljubljana, said the protesters gathered to "show what they did in secret without telling the people. This is a disgrace for the Slovenian nation, we cannot allow this."
Some of the protesters wore the signature Guy Fawkes masks, the symbol of hacker group Anonymous, which has joined the anti-ACTA camp.
Protesters took turns on the megaphone to explain their opposition. One protester said: "We are protesting against ACTA and against the vassal political class which has once again bowed to corporations and financial markets."
The rallies are the result of a Facebook initiative, in what is another in a series of recent, albeit smaller, grassroots protests to have originated on social networks.
Like in most of the 22 EU member states which signed ACTA, critics have been warning against the unacceptable control of web traffic on the part of organisations concerned merely with profit, the filtering of internet traffic which will open the door to privacy invasion, and restrictions to innovation.
Another issue highlighted by opponents has been the clandestine fashion in which the agreement was adopted, with calls spreading now for a wide public debate before the decision on ratification in parliament.
These calls were welcomed by the Slovenian government, which however like the European Commission rejected the view that procedures so far have not been transparent.