The Spanish state weather agency AEMET confirmed the record on Sunday, as both Spain and Portugal endure an unusually early and intense northern hemispher summer heatwave.
Spain's previous June high of 45.2C was set in Seville in 1965.
Dozens of towns and cities across Spain reported maximum temperatures above 40C while neighbouring Portugal also sweltered.
In the country's southern Algarve tourist region, highs reached about 40C.
On Spain's holiday island of Mallorca, temperatures climbed to nearly 35C.
Overnight conditions offered little relief.
In southern Spain, night-time lows remained above 30C - a level of sustained heat that experts say can pose serious health risks.
Locals are accustomed to coping with extreme temperatures by limiting outdoor activity during peak heat, wearing light clothing and hydrating frequently.
But the combination of scorching heat and intense sun is rapidly drying out soil and vegetation, sharply increasing the risk of wildfires.
Meteorologists warn that such heatwaves are becoming more frequent and arriving earlier in the season due to human-driven climate change.
According to meteorological agency AEMET, only two heatwaves were recorded in June between 1975 and 2000.
Between 2000 and 2024, that number rose to nine.
This year, temperatures approached August levels as early as late May.
7°C