Purpose: To summarize the evidence regarding the acute and chronic effects of interval training (IT) in the immune system through a systematic review with meta-analysis. Design: Systematic review with meta-analysis. Data source: English, Portuguese and Spanish languages search of the electronic databases Pubmed/Medline, Scopus, and SciELO. Eligibility criteria: Studies such as clinical trials, randomized cross-over trials and randomized clinical trials, investigating the acute and chronic effects of IT on the immune outcomes in humans. Results: Of the 175 studies retrieved, 35 were included in the qualitative analysis and 18 in a meta-analysis. Within-group analysis detected significant acute decrease after IT on immunoglobulin A (IgA) secretory rate (n = 115; MD = −15.46 µg·min⁻¹; 95%CI, −28.3 to 2.66; p = 0.02), total leucocyte count increase (n = 137; MD = 2.58 × 10³ µL⁻¹; 95%CI, 1.79 to 3.38; p < 0.001), increase in lymphocyte count immediately after exercise (n = 125; MD = 1.3 × 10³ µL⁻¹; 95%CI, 0.86 to 1.75; p < 0.001), and decrease during recovery (30 to 180 min post-exercise) (n = 125; MD = −0.36 × 10³ µL⁻¹;−0.57 to −0.15; p < 0.001). No effect was detected on absolute IgA (n = 127; MD = 47.5 µg·mL⁻¹; 95%CI, −10.6 to 105.6; p = 0.11). Overall, IT might acutely reduce leucocyte function. Regarding chronic effects IT improved immune function without change leucocyte count. Conclusion: IT might provide a transient disturbance on the immune system, followed by reduced immune function. However, regular IT performance induces favorable adaptations on immune function.