This is a really interesting question, which unfortunately probably won't get a lot of responses.

As with many other questions comparing two very different regions, the answer is complex. To summarize a response: there was an awful lot of medicine going on in (say) 18th and 19th century pre-colonial West Africa, but most of it wouldn't have been recognizable to 19th century Europeans as medicine.

A starting place for understanding this is probably Steven Feierman and John Janzen, eds., The Social Basis of Health and Healing in Africa. That term "social basis" is important. Most healing practices in pre-colonial West Africa were based on the assumption that disease was a result of imbalances or impurities in social, political, and cultural relationships. In other words, one was sick largely because one's relationships with the ancestors or others had been mismanaged or were otherwise off-kilter. This might mean one had transgressed some kind of cultural value or norm. Often, this was seen as a community problem and needed a community solution, and so people were called together to find solutions. Thus healing might mean searching around for social wrongs that had happened or mistakes one had made or deals one had broken or even evil people who were trying to exact revenge (i.e. witches, but this probably operated quite differently than we assume).

Since late 19th century western medicine largely assumed complete separation of the body from the social circumstances, missionaries and other Europeans who arrived at that time misunderstood most medical practices prevalent in West Africa. Ironically, we now understand better the value of relationships to health, so you might say we are better able to value social healing in an African context!

I recognize that you might have wanted to know more about mudpacks for open wounds and early cowpox vaccinations for smallpox (both of which existed in pre-colonial Africa), but I don't know as much about those. Sorry.