In the absence of reliable and timely weather information, unprecedented weather shocks can influence farmers’ decision-making. We take the case of Uganda to investigate the relationship between weather shocks and temporary migration among smallholders. Using longitudinal data from a nationally representative survey – Living Standard Measurement Study-Integrated Survey in Agriculture (LSMS-ISA) –, we examine if household-level weather shocks affect temporary migration. Using panel data estimators, we show that weather shocks reduce temporary migration among poor households, and the relationship is more pronounced for smallholders. We also find that the relationship differs by the type of migration. Weather shocks reduce temporary labor migration and migration for educational purposes, but migration for other reasons is not affected. These results are confirmed by focused group interviews with 24 rural farmers from all four regions of Uganda. We identify reduced agricultural productivity and low farm revenue as potential channels for the negative relationship between weather shocks and migration.