Dr Upton was the driving force behind the early design of the credit-card sized computer and founded the charity that oversees its development.
The Pi has proved hugely popular with electronics hobbyists and many children are using the devices to get a taste of computer coding.
In April 2016, the Pi became the most popular British computer ever made.
More than eight million have been sold since the tiny device was launched in early 2012. The small computer has gone through several revisions and the most recent update, version 3, has a 64-bit processor and wi-fi and Bluetooth built in.
Dr Upton said he was "shell-shocked" to receive the honour. He said it was a tribute to the team of people at the Raspberry Pi Foundation and its electronics partners who were working on the device and the educational projects it has kicked off.
In total, he said, 200 people at the Foundation, chipmaker Broadcom, electronics suppliers Farnell and RS Components and Sony were involved with the Pi.
"We're starting to make real progress on our mission," he told the BBC "There are over 4,000 Code Clubs in UK schools, nearly 800 Raspberry Pi Certified Educators and more applicants for computer science at Cambridge than at the height of the dotcom boom."
Several other technology industry veterans were also honoured in the list. Dr David Grant, head of Welsh electronics firm IQE Semiconductors, was made a knight for services to engineering and technology.
Dr Jo Twist, head of the games industry body UKIE, was made an OBE, as was Sarah Wood, chief executive of video ad firm Unruly.
Sarah Bestwick from games publisher Team 17, Shazam boss Andrew Fisher and Tech Crunch editor Mike Butcher all became MBEs in the list.
Eben Upton, pioneer of the Raspberry Pi bare-bones computer, has become a CBE in the Birthday Honours list.