The suspect, also 17, who cannot be named because of his age, is due before Salisbury Magistrates' Court on Tuesday.
Ellie, a Year 12 pupil at Hardenhuish School, was pronounced dead after emergency services were called to a house on Friday afternoon.
The suspect was detained in the nearby town of Chippenham later that evening.
"I would like to again thank the communities of Calne and Chippenham for the support and patience they have shown so far to our officers as they have carried out inquiries as part of this murder investigation," said Wiltshire Police inspector Don Pocock. "A case like this takes time and will understandably have an impact on the local community - so thank you for your help and understanding.
"Over the past few days, people living in Calne and Chippenham would have seen an increased police presence which I appreciate can add more anxiety and upset to what is already a tragic situation. However, I want to reassure everyone that the officers and detectives involved have been working hard to carry out their duties as swiftly as possible to minimise the impact on those living and working here.
"Inevitably there has been a lot of interest and discussion into this case on social media and the like - however, now that a person has been charged and court proceedings have started, please be mindful not to speculate or comment publicly on anything to do with the investigation."
Lisa Percy, head teacher of Hardenhuish School, said: "I would like to thank everyone for all of the messages of support that we have received from past, present and future parents, colleagues and other members of the community. We would like to express our thanks to all partner agencies who have supported us too.
"The students, staff and parents have found comfort in being together and paying their respects to Ellie and our thoughts remain with her family and friends at this time."