Few studies have characterised the degree of engagement in transactional sex among men and transgender women who have sex with men and explored its association with sexually transmitted infections and human immunodeficiency virus in Ecuador. We screened 642 men who have sex with men and transgender women for a pre-exposure prophylaxis clinical trial (iPrEx) in Guayaquil, Ecuador, 2007–2009. We analysed the association of degree of engagement in transactional sex and prevalence of sexually transmitted infections including human immunodeficiency virus using chi-square and analysis of variance tests. Although just 6.2% of those who screened self-identified as sex workers, 52.1% reported having engaged in transactional sex. Compared to those who had never been paid for sex, those who had been paid were more likely to have a sexually transmitted infection (56.6% vs. 45.0%, p = 0.007) and trended towards a higher human immunodeficiency virus prevalence (16.6% vs. 10.4%, p = 0.082) at screening. Transgender women compared to other men who have sex with men were more likely to have sexually transmitted infections diagnosed at screening (75.6% vs. 50.0%, p = 0.001). Transactional sex is practiced widely but occasionally among the men who have sex with men and transgender women in Guayaquil who screened for the iPrEx study; however, engaging in transactional sex may not lead to a sex worker self-identification. Both transactional sex and being a transgender woman are associated with sexually transmitted infections prevalence.