Yes. You can run cron jobs in N99panel.
To run a cron job, you would need to do two things
1. Create/Update cron jobs from within List Users >> User >> User Cron
2. Enable CronD from within List Users >> User >> Manage SSHD/CronD
The cron daemon/process uses UTC time. Therefore you would need to accordingly adjust time/period values of your cron entries.
Also to the cron daemon/process the entire user directory tree with all VHosts/Websites gets exposed.