The 33-year-old football player, who currently plays for Greenock Morton in the Scottish Championship, is set to appear before Carlisle Magistrates on Thursday. He is facing charges of importing class B drugs.
Around 60 kilos of cannabis was found in two suitcases that arrived from Bangkok last month, with two women also charged before being released on bail.
Emmanuel-Thomas - who started his career at Arsenal before playing for Ipswich, Bristol City, QPR, Livingston and Aberdeen - was detained in Inverclyde on Wednesday in an operation supported by officers from Police Scotland.
News has contacted Greenock Morton, who have not commented on the matter.
National Crime Agency senior investigating officer David Phillips said: "The NCA continues to work with partners like Border Force to target those involved in drug smuggling - that includes both the couriers and the organisers.
"We would appeal to anyone who is approached to engage in any kind of smuggling to think very carefully about the likely consequences of their actions, and the potentially life-changing risks they will be taking."
In August, the NCA issued a warning to travellers arriving into the UK from Thailand, Canada and the United States that they face jail sentences of up to 14 years if caught attempting to bring cannabis into the country after a huge upsurge in arrests.