Mikayla Haining died on Thursday June 8 after being taken to Raigmore Hospital in the Highland city.
Police Scotland initially said the death was unexplained as officers tried to established the circumstances, but earlier this week it was confirmed that the death was being treated as suspicious.
Officers described it as a “complex investigation”.
A 19-year-old man has now been charged in relation to the death.
He is expected to appear at Inverness Sheriff Court on Thursday.
Detective Inspector Brian Geddes said: “Following the death of 3-week-old Mikayla Haining, I can confirm a 19 year-old man has been charged and reported to the Procurator Fiscal”.
“This has been a complex investigation and it remains ongoing. I would like to thank the community for their patience while these enquiries have been, and continue to be carried out.”