The press freedom group said 19 were killed in Syria alone, followed by 10 in Afghanistan, nine in Mexico and five in Iraq.
Almost all of those killed were locally-based journalists.
Although it was fewer than the 67 killed in 2015, the group put the decrease down to "the fact that many journalists have fled countries that became too dangerous, especially Syria, Iraq, Libya, Yemen, Afghanistan and Burundi".
It said the withdrawal of reporters from these conflict-ridden countries had created "news and information black holes where impunity reigns".
Nine bloggers and eight media workers have also been killed this year.
Reporters Without Borders said the fall in deaths was also the result of the "terror" imposed by what it called "press freedom predators" who close media outlets arbitrarily and gag journalists, AFP reported.
In countries such as Mexico, this led to journalists self-censoring to avoid being murdered, the group said in its annual report.
In Afghanistan, all of the 10 journalists killed were deliberately targeted because of their profession.
Seven, including three women, were killed in a suicide attack in January on a minibus used by privately-owned Tolo TV. The Taliban claimed responsibility.
Yemen, where more than 7,000 people have been killed since 2015 in a war pitting Saudi-backed regime forces against Houthis was another a black spot for journalists with five killed.
"The violence against journalists is more and more deliberate," RSF secretary-general Christophe Deloire said.
"They are clearly being targeted and murdered because they are journalists.
The group called for incoming UN Secretary-General Antonio Guterres to appoint a special representative for the protection of journalists.