WhiteBoxTools has RootMeanSquareError tool. QGIS 3.x can access WBT through WhiteBox for Processing plugin. Definitely worth a try.
Unfortunately this RootMeanSquareError tool did not work for me when I tested it in my environment (QGIS 3.4.4 on Windows10). So let me suggest another approach, using R through Processing R Provider plugin.
You will need to install
Processing R Provider plugin, but its setup is really easy.
Then click on big R icon on top of the Processing Toolbox panel, to activate
Create New R Script.
In the blank window, please copy and paste texts below:
##Raster_Statistics= output table
delta <- (Input_Raster - Base_Raster)^2
RMSE <- sqrt(cellStats(delta, 'mean'))
Result <- data.frame(rbind(RMSE), row.names= c("RMSE"))
colnames(Result) <- c("Stats")
Raster_Statistics <- Result
If you click on green triangle icon (
Run Script) you will get a new window. Assign each of your raster layer to
Input Raster and
Base Raster and run the tool.
It will add a new table layer
Raster statistics with the calculated RMSE. Open its attribute table to see the result.