Abstract: The effects of the forms for the end cap boundary conditions were discussed in the solution of the flow field of a gas centrifuge by using the Onsager’s pancake model. The end cap boundary conditions have two forms, one of which is formulated from the analysis of the horizontal Ekman boundary layers on an end cap (referred to as the original form), and another is derived from differentiating the original form (referred to as the derivative form). The form currently in use is the latter. However, the differentiation operation results in the loss of information in the boundary conditions of the original form, and the complication of the conditions. In the cases of thermal drive and end cap feed, the differences were analyzed in the flow fields obtained by using the two forms of boundary conditions. The results show that, in general, the flow fields are different when using different forms. To avoid loss of information in the derivative form, the use of the original form is recommended.