If you have System Center Configuration Manager 2012/2012R2 and you want to upgrade to the latest package 1606 you first have to upgrade to 1511. This should be the last upgrade you’ll need to manually perform, after you can upgrade straight from the SCCM console itself. Thank you Microsoft!
The supported in-place upgrade paths are below, more details found here.
Upgrading from SCCM 2012 to 1511 is straightforward. Before starting your installation of 1511, download this patch from Microsoft and install it.
Download and install Windows 10 ADK even if you don’t have Windows 10 in your environment yet, because you will soon enough. Choose based on your version of Windows 10, the latest is 1607 at the time of writing.
Check that are using a supported version of SQL Server and then download and install SCCM 1511. We downloaded it from Microsoft VLSC because we have a volume license account with Microsoft. If you need an evaluation copy you can find the current branch here.
Install package, you know how this works. Just keep selecting Next, no surprises.
I suggest restarting your server after completion just for peace of mind.
After your SCCM server has a chance to sit for a bit it will automatically download builds 1602 and 1606. Go to Administration > Cloud Services > Updates and Servicing to view.
Note if it gets stuck in “Downloading” for too long, open Services.msc and restart the service named “SMS_EXECUTIVE” and downloading will resume.
If you wait for a while (less than 30 minutes), then restart your server you will get a popup that lets you know the latest version is available for download.
Install Update Pack from the console, you can skip to 1606.
The steps are again really boiler plate, just keep selecting Next.
Once installation is complete, then force update your client agents. Go to Administration > Site Configuration > Sites > Hierarchy Settings
If interested here is additional documentation from Microsoft.
Call it a day!