The botanical garden in Troja is situated near the Prague ZOO. Unlike the central one, is is situated a little bit in the outskirts of the city. Nevertheless you can reach it easily by public transport (subway and bus). The garden is open throughout the year and in my opinion is the prettiest in spring and autumn.
The outdoor exhibition is a large area of 25 hectares in total. It consists of several parts including eg. an ornamental garden, a Mediterranean flora area, a vineyard (with a wine cellar and nice view over Prague), a peat bog with a small lake, a Japanese garden and much more – it depends on what you like and what you are in the mood for :-).
As the season changes, there are also topical exhibitions (pumpkins, bonsai etc.)
When visiting the outside exposition, you can also refresh yourself – some weekends there is a mobile tea house present serving a nice selection of teas. Recently a brand new bistro opened just in the middle of the garden – you can get there some plant-based snacks and beverages.
Another part of the botanical garden worth a visit (you have to pay a separate fee or buy a combined ticket) is Fata Morgana – a gigantic greenhouse.