Yes, you can register a study on ClinicalTrials.gov at any time. Please note that, in general, Section 801 of the Food and Drug Administration Amendments Act (FDAAA 801) requires Applicable Clinical Trials to be registered within 21 days of enrollment of the first participant. In addition, the International Committee of Medical Journal Editors and other journals require registration of clinical trials prior to enrollment of the first participant.
See FDAAA 801 Requirements for more information.