Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are being administered around the world; however, lactating women were excluded from SARS-CoV-2 vaccine trials. Therefore, knowledge about the effect of vaccination in this specific group is limited. This information is essential to empower lactating women to make a well-informed decision on their choice for vaccination. After natural infection, SARS-CoV-2 specific antibodies are present in human milk, which might offer protection for her newborn. The dynamics of these antibodies in human milk following vaccination remain to be elucidated. Research Aim: To determine the effect of vaccination with BNT162b2 on the levels of SARS-CoV-2 specific IgA in human milk. Methods: In this prospective longitudinal study, we included lactating women who received the BNT162b2 vaccine. Human milk samples were collected prior to vaccination and 3, 5, 7, 9, 11, 13, and 15 days after both vaccine doses. Samples were analyzed using enzyme-linked immunosorbent assay against the spike protein of SARS-CoV-2. Results: In total, 366 human milk samples from 26 lactating women were analyzed. A biphasic response was observed, with SARS-CoV-2 specific immunoglobulin A (IgA) starting to increase between day 5 and 7 after the first dose of the vaccine. After the second dose, an accelerated IgA antibody response was observed. Conclusion: After vaccination with the mRNA-based BNT162b2 vaccine, a SARS-CoV-2 specific antibody response was observed in human milk. The presence of SARS-CoV-2 specific IgA after vaccination is important as antibodies are transferred via human milk, and thereby might provide protection to infants against COVID-19.