McKenna and the Sochi bronze medallist will share time with the toddler over the next four months.
Monday's agreement came shortly before both parents were to testify at a Manhattan Family Court hearing.
Miller declined to comment. McKenna says it's best the hearing will wait until more facts are gathered.
The case spurred concern among women's rights activists last year. A judge said McKenna had been "irresponsible" by moving while pregnant to New York from California.
Miller lives in California and claimed paternity there. McKenna moved to attend Columbia University.
A New York appellate court overturned that ruling. The dispute has been in both California and New York courts.