This study aimed to assess whether educational level is an independent determinant for sexually transmitted infections (STIs) among clients consulting Dutch sexual health centres (SHCs). With data from the National STI surveillance database (2015–2017), generalized estimating equations corrected for (sexual) risk factors were used to estimate associations between educational level and chlamydia and gonorrhoea among women ( n = 146,020), heterosexual men ( n = 82,882) and men who have sex with men (MSM) ( n = 52,149) and syphilis and HIV among MSM. Compared to the highest educational level (bachelor/master), all lower educational levels were associated with gonorrhoea among women (adjusted odds ratio 1.40; 95% CI 1.18–1.66 for higher general/pre-university level to 3.57; 95% CI 2.66–4.81 for no education/elementary school level) and heterosexual men (respectively 1.36; 1.06–1.74 to 3.84; 2.89–5.09). Women with no education/elementary school level (1.37; 1.17–1.62) and heterosexual clients with (pre-)vocational secondary educational level were more likely to test positive for chlamydia (women: 1.43; 1.39–1.48 and heterosexual men: 1.31; 1.26–1.37) than clients with higher general/pre-university level or bachelor/master level. In MSM, (pre-)vocational secondary educational level was associated with chlamydia (1.16; 1.11–1.22), gonorrhoea (1.15; 1.10–1.21) and syphilis (1.18; 1.08–1.29), and both (pre-)vocational secondary educational level (1.48; 1.25–1.76) and no education/elementary school level (1.81; 1.09–3.00) were associated with HIV. Lower educational levels were independent determinants of STI in SHC clients. Sexual health centres could facilitate STI testing and care among lower educated people by prioritizing their access.