It is important to time evaluation activity carefully. First, determine whether you are planning formative or summative evaluation (see The Purpose of Evaluation). Formative evaluation takes place during the project; summative evaluation at the end of the project or of a major phase of work.
Formative evaluation of the project's processes is ongoing: this includes questions about project management; project progress against milestones; and dissemination of findings & learning.
Formative evaluation of outcomes and impact needs to be timed carefully so that on the one hand there has been enough time elapsed and enough work done for products to have emerged and been delivered/used; and on the other hand there is enough time left for evaluation findings to influence the remainder of the project.
Summative evaluation needs to be timed for the end of the project or of each major phase. Bear in mind that resourcing summative evaluation after the formal end of the project could be problematic.
One other consideration is that it may be helpful to try to time your evaluation to coincide with that of other related projects. You can then compare your findings and your methodologies (though taking care to ensure that comparisons are really valid!).