First, note that there are options for embedded systems with 32-bit CPUs to be Y2038 compliant without resorting to 64-bit CPUs. For example, a 32-bit embedded system may be able to use a 64-bit time library, or a time library with 32-bit unsigned time_t to handle dates through 2106.
Below are some 64-bit CPUs already available. 64-bit CPUs are an area of active development, so this information may become out of date quickly.
Broadcom BCM2837 – This quad-core 64-bit SoC is based on ARM Cortex-A53 and runs at 1.2GHz. It can be used for mobile devices, but it is also intended for general purpose usage. Most notably, it is the processor used in Raspberry Pi 3 which was recently announced in Feb 2016. The Raspberry Pi 3 is very impressive, at ~10x the performance and the same cost (~$35 US) as the first Raspberry Pi (which was based on a 32-bit processor and therefore susceptible to Y2038). However, all currently available operating systems for the Raspberry Pi are 32-bit. See this link for additional discussion.
Allwinner A64 – This chip is also based on ARM Cortex-A53, with a price of around $5. It is the processor being used in the Pine64, which is also impressive, selling for as little as $15.
HiSilicon Kirin 6220 – An 8-core SoC based on ARM Cortex-A53 at 1.2GHz. Used in the HiKey dev board which sells for around $99 depending on configuration.
Qualcomm Snapdragon – The 800, 600, and 400 series Snapdragon processors are almost all capable of running in 64-bit mode. Below are several of the available development boards:
- DragonBoard 410c from Arrow Electronics for $75
- Open-Q 600 from Intrinsyc for $165
- DragonBoard 810 from Intrinsyc for $495
Nvidia Tegra K1 – This processor is used on the Google Nexus 9 tablet
Nvidia Tegra X1 – This processor is used in the Google Pixel C Chromebook
MediaTek MT6752– Another processor intended for mobile devices
All of the above products are based on technology from ARM Holdings. ARM offers a variety of 64-bit designs which it licenses to other companies.
Intel offers many variations of 64-bit CPUs with “Embedded Options Available”. These can be listed and compared using the selection guide/chart here.
AMD offers some 64-bit CPUs for embedded use. The Wikipedia page here has a useful table.