The Holy Trinity of Marx, Lenin and Engels. I think the death toll from this exquisitely atheistic and
secular philosophy/religion took about 150 million lives.
Not really a religion, per se. If we're including state driven stuff as well, capitalism is right up there, considering the numbers of dead from the New World Conquest... or can those deaths be ignored because they were long ago and didn't really affect our cultural forebears? Also about 40 million of the deaths offten attributed to Communism were actually due to Axis power fascists, although they often get pinned on Stalin because he was in charge at the time. Similar things happen when looking at Mao's body count. The Chinese Civil War was extremely bloody, but is it really accurate to pin all those deaths on one side? Culpability in these things is often more complex than a nice ideology confirming "the ideology I hate did the bad thing in a vacuum".
Pretty sure the estimates of deaths under the Mongol invasions are right up there, too, but I'd have to look it up.
Maybe the lesson here is that ideologies and religions aren't violent, people are, and will try to use ideology/religion as either justification or simplistic explanation?
Edit:looks like the general estimates for the Mongol invasions are ~ 40, 000, 000 also worth mentioning the Tai Ping rebellion in China in the 1800s, which was led by a nominal Christian, and led to an estimated ~30-40, 000, 000 civilian deaths.