Introduction: In the 2000s, the Baltic countries experienced unprecedented economic growth followed by a deep recession. This study aimed to examine changes and educational inequalities in suicide mortality among working-age men in the Baltic countries and Finland in relation to macroeconomic fluctuations. Methods: We analysed changes in overall suicide mortality and by educational level between the 2000–2003, 2004–2007, 2008–2011 and 2012–2015 periods among men aged 30–64 years using census-linked longitudinal mortality data. We estimated age-standardised mortality rates, mortality rate ratios (Poisson regression), the relative index of inequality and slope index of inequality. Results: Overall suicide mortality fell markedly from 2000–2003 to 2004–2007. The decline was largest among high educated men in the Baltic countries and among middle and low educated men in Finland. From 2004–2007 to 2008–2011, the positive trend slowed and while suicide mortality continued to fall among middle and low educated men, it increased somewhat among high educated men in all Baltic countries. In Finland, suicide mortality decreased among the high educated and increased slightly among low educated men. Conclusions: In the Baltic countries, lower educated men had a smaller decline in suicide mortality than higher educated men during a period of rapid economic expansion, however, they were not more disadvantaged during the recession, possibly because of being less exposed to financial loss. Consequently, relative inequalities in suicide mortality may increase during economic booms and decrease during recessions.