CR means slightly different things in Pathfinder and 5e. I look at the CR of the Pathfinder encounter and determine, based on Pathfinder's guidelines, how great a challenge the encounter is (Easy, Average, Challenging, Hard, Epic). Then I use the Kobold Fight Club calculator to ensure that the encounter is the same difficulty for PCs of the applicable level in 5e.
It's a little more time consuming, but if you want to be consistent I've found it to be the best way.
Note that some creatures have radically different CRs between the games, so beware.