the only big brewery in Prague that offers Tours is Staroprammen and it has been a long time since I did a tour, from what I can gather it is now more of a visitor experience rather than an actual tour, but have a look.
http://www.staropramen.com/age%20gate?retUrl=/en/
http://en.ufleku.cz/program/brewery-tour-u-fleku/
this is a small brewery pretty near the centre, never done a tour but been for beer there many times.
http://beertours.cz/
this company organises tours to U Fleku and U Medvidku, but you can go to the upstairs brewery in U Medvidku and try their beers and you sit in the room where the beer is brewed stored and poured, I often pop in there for a few beers when I am in the city.
https://czechbeertours.com/
another link for beer tastings and tours but I don't think any of them actually do a brewery tour but have a look.
https://www.praguebeergarden.com/pubs/category/microbreweries
this is a link to loads of micro-breweries so have a look ,in many you will be sitting in the areas near to where the beer is produced and often see what is going on.Lod Pivovar mentioned is my new favourite place in the city, the down-stairs part you are actually sitting beside the brewing kettles, great food and superb beer.
for something a bit different try this.
https://www.livingpraguetours.com/tour/czech-pubs-and-tapas/
not sure what pubs you will be taken into will probably vary from tour to tour but I know Jason that runs the tours very well and he knows his Prague pubs.if you look at some of the photos you just might see me there.
so lots of options and hopefully this has helped.
when are you visiting?