The Health Ministry authorized the operations last year, but none has been performed since. It was unclear when the surgeries would begin.
Castro also said she backs efforts to allow lesbians to be artificially inseminated, a procedure currently barred.
The first successful sex-change operation was performed on the island in 1988, but subsequent procedures were prohibited, Mariela Castro told an international congress on assisted reproduction meeting in Havana.
Some Cubans protested the decision last year to allow the operations, either because of general opposition to the procedure or for its high costs for a developing country with economic problems.
The government would bear the cost of the operations because Cuba has a universal health care system.