The apparent ban for Edward Leung, of the Hong Kong Indigenous party, from the September vote came despite him signing a controversial new form declaring Hong Kong is an "inalienable" part of China.
Critics have slammed the new stipulation by electoral authorities as political censorship and an attempt to deter prospective candidates from advocating self-determination or independence from Beijing.
Some activists are calling for more distance or even a complete breakaway from the mainland as fears grow that freedoms in the semi-autonomous city are disappearing due to Beijing interference.
Leung, 25, eventually signed last week, despite his open advocacy for an independent Hong Kong, in the hope the authorities would validate his candidacy.
Also Read
But he said he had been barred from standing.
"This election is a dark election, an election that is being controlled," Leung told reporters today.
"Every day Communist China rules (Hong Kong)... I won't be able to enter the Legislative Council. So what else can I do? Revolution!"
His party accused the electoral commission of "trampling the will of the people, abusing administrative power and giving up political neutrality".
The statement added a government officer handling Leung's case had explained she did not believe he had changed his pro-independence stance when notifying him by email that his application had been unsuccessful.
Leung later walked into a government briefing for election candidates and raised his middle finger at the speakers before departing to cheers and chanting from hundreds of supporters outside, some of whom wore balaclavas.
Other pro-democracy politicians also walked out of the meeting carrying banners saying "Defend fair elections".