There are 3 books in the The Apothecary Series series. The newest book is The After-Room which came out in 2015.

1
The Apothecary

By Maile Meloy , Ian Schoenherr (illustrator) ,

Book cover of The Apothecary
A dose of magic could save the world . . .

Fourteen-year-old Janie Scott is new to London and she's finding it dull, dreary and cold - until she meets Benjamin Burrows who dreams of becoming a spy. When Benjamin's father, the mysterious apothecary, is kidnapped he entrusts Janie and…
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2
The Apprentices

By Maile Meloy , Ian Schoenherr (illustrator) ,

Book cover of The Apprentices
It’s 1954, and Janie Scott is in boarding school in New Hampshire, trying to make a new life. Two years have passed since she last saw the mysterious apothecary—or his defiant son, Benjamin. All she knows is that her friends are out there somewhere, trying to keep the world safe…

3
The After-Room

By Maile Meloy , Ian Schoenherr (illustrator) ,

Book cover of The After-Room
It's 1955, and Benjamin Burrows and Janie Scott are trying to live a safe, normal life in America. It's not easy, when they have the power to prevent nuclear disaster, and sinister forces are circling. Soon the advice of a mysterious, unscrupulous magician propels Janie and Benjamin into danger, and…