Estimating COVID-19 vaccine effectiveness (VE) by time since vaccination (TSV) is essential for understanding how protection may change over time and enables meaningful comparisons across studies. This is important for accurate comparisons of VE against different SARS-CoV-2 variants/sublineages, across age groups, during different periods post vaccination campaign, or by vaccine type/brand. We provide recommendations for case-control VE studies on estimating and reporting VE analyses by TSV, with the aim of improving quality of these estimates. Our recommendations cover study design and pre-analysis considerations, descriptive analyses, choice of categories of TSV, categorical and continuous modeling approaches, and best practices for reporting VE by TSV. Using a real-life case-control study, we apply these recommendations and include accompanying statistical scripts in R and Stata. These recommendations will serve as a practical resource for researchers conducting VE analyses by TSV. We encourage ongoing refinement of them through input from other study groups.