They mean the same thing in most cases, but with a They mean the same thing in most cases, but with a little difference in flavor. In some cases, "in fact" is used when some news or situation that we know about is not true. "He said he had been at work, when in fact, he had left work early." You would not use "in effect" in such a case. "In effect" describes a situation where the consequences of some action or occurrence need to be explained. "The council voted down the new road, in effect stopping further houses being built on the beech."

and "in practise"?