Background: Some evidence suggests that forests attract rain and that deforestation contributes to changes in rainfall and temperature. The evidence, however, is scant, particularly on smaller spatial scales. The specific objectives of the study were: (i) to evaluate long-term trends in rainfall (1970–2009) and temperature (1981–2009) and their relationships with change in forest cover, and (ii) to assess the influence of remnant forests and topographical factors on the spatial variability of annual rainfall. Methods: This study investigated the forest-rainfall relationships in the Central Rift Valley of Ethiopia. The study used 16 long-term (1970–2009) and 15 short-term (2012–2013) rainfall and six long term (1981–2009) temperature datasets. Forest and woodland cover decline over the past 40 years (1970–2009) and the measured distances between the remnant forests and rainfall stations were also used. The long-term trends in rainfall (1970–2009) and temperature (1981–2009) were determined using Mann-Kendall (MK) and Regional Kendall (RK) tests and their relationships with long-term deforestation were evaluated using simple linear regression. Influence of remnant forests and topographical variables on the spatial variability of rainfall were determined by stepwise multiple regression method. A continuous forest and woodland cover decline was estimated using exponential interpolation. Results: The forest and woodland cover declined from 44% in 1973 to less than 15% in 2009 in the Central Rift Valley. Annual rainfall on the valley floor showed an increase by 37.9 mm/decade while annual rainfall on the escarpments/highlands decreased by 29.8 mm/decade. The remnant forests had a significant effect (P-value <0.05, R2 = 0.40) on the spatial variability of the number of rainy days observed over two years (2012–2013), but had little effect on the variability of rainfall distribution. For the total annual rainfall, slope was the best predictor which explained 29% of the rainfall variability in the Central Rift Valley. For the annual number of rainy days, both slope and elevation explained most of the variability (60%) of annual number of rainy days. Conclusion: This study did not find a significant correlation between long-term rainfall trend and forest and woodland cover decline. The rift valley floor warmed significantly due to long-term deforestation in the Central Rift Valley. Topographic factors play a significant role than forest cover in explaining the spatial variability of annual rainfall in the long-term and short term time scale in the Central Rift Valley. But, the short-term rainfall data indicated that the remnant forest had a significant effect on the spatial variability of the number of rainy days.