The first analog to digital converter was flown on board Injun 1 on June 29, 1961. It was also the first spacecraft completely designed and built by a university--in this case, the University of Iowa.
From "The Origins of Space Radio and Plasma Wave Research at the University of Iowa" by Donald A. Gurnett:
At the suggestion of a newly hired Assistant Professor, Brian J.O'Brien, I was urged to start thinking about a spacecraft-borne “encoder” that would transfer the "0s" and "1s" in the binary counter to a corresponding serial sequence of "0s" and "1s" that could be transmitted to the ground. I did this by finding a very simple method of converting the binary counter (often called an accumulator) into a shift register using a voltage control line that had only one resistor and one diode per stage in the counter. This system is now called a “shifting accumulator,” and was later the subject of a patent application by the Office of Naval Research. By using one shifting accumulator for each particle detector, I devised an encoding system that could produce a binary data stream from an arbitrary number of detectors. Analog voltages, such as battery voltages, could also be encoded by the simple addition of an analog-to-digital converter.
Gurnett goes on to describe the encoding system used on Injun 1:
Using frequency-shift-keying between two modulation frequencies, 3.072 and 4.096 kHz, which represented the “0s” and “1s,” this encoder provided digital data at a bit rate of 256 bits/s from thirteen particle detectors and an auroral photometer [O’Brien et al., 1962]. Injun 1 was one of the first spacecraft to use an entirely digital data system and was the first in a series of five low-altitude polar-orbiting spacecraft built at Iowa, later known as the “Injun” series of satellites.