Brew Lab, which is based on College Street in the capital, was one of only five venues in the UK picked out in the list.
The votes were cast in a poll of readers of travel website Big7 across their 1.5million strong community on social media and by a panel of coffee experts, with online reviews, previous media coverage and notable blogs also included in the overall rating.
Jonas Reindl, a specialist coffee shop in Vienna, Austria, was named the best in Europe.
Two stores in London - Kaffeine (47) and Dark Arts (48) - and one in Brighton (Small Batch Coffee Roaster, 49) and one in Manchester (Takk, 46) were named alongside Brew Lab, which placed 50th on the list.
Posting on their website, the team at Big7 wrote: "With a third wave of coffee creativity sweeping across Europe, we wanted to share the very best coffee shops across the continent.
"From independent coffee hatches serving out flat whites through a window to motorcycle stores/roasteries, these are are the best spots across Europe to get your caffeine fix."
Brew Lab was praised for serving the "best coffee in the city", its uniqueness and the fact that its coffee menu features four rotating single-origin coffees: two brewed on their brew bar as pour-overs, and two on their espresso bar.