According to a paper by Depetris-Chauvin and Weil, the answer is no.
Here is the abstract:
We examine the effect of malaria on economic development in Africa over the very long run. Using data on the prevalence of the mutation that causes sickle cell disease, we measure the impact of malaria on mortality in Africa prior to the period in which formal data were collected. Our estimate is that in the more afﬂicted regions, malaria lowered the probability of surviving to adulthood by about ten percentage points, which is twice the current burden of the disease. The reduction in malaria mortality has been roughly equal to the reduction in other causes of mortality. We then ask whether the estimated burden of malaria had an effect on economic development in the period before European contact. Using data at the ethnic group level, we ﬁnd little evidence of a negative relationship between malaria burden and population density or other measures of development.\
And here’s a summary of the main finding:
With estimates of the extent of malaria mortality in hand, we then turn to look at the impact of the disease on economic development. We present regressions of a number of measures of development within Africa on a malaria burden measure that we create based on sickle cell prevalence. Of particular note, we apply our analysis to a data set measured at the level of ethnic groups as an alternative to more common country-level analyses. We present simple OLS results, as well as results in which we instrument for malaria burden, using an index of climactic suitability for malaria transmission. The result of this statistical exercise is that we find no evidence of malaria burden negatively affecting historical economic development.