Point and click installation

In Central Administration, under System Settings, click Manage Services on Server.
Start Secure Store Service (link on the right side).
Click Application Management (left menu) and under Service Applications, Manage service applications, New (top, left), Secure Store Service Application and fill out the page as follows:

Name: <Secure Store Service Applcation Name>
Click Register new managed account and fill out the page as follows:
Username: <domain>\<Managed Account>
Choose to, enable or disable automatic password change and click [OK].
Database, Database Name: <EnvironmentPrefix>_SharePoint_SecureStore_service.
Application Pool, Application pool name: <Secure Store Application Pool Name>
Configurable: <domain>\<SecureS> and click [OK], [OK].

Click <Secure Store Service Application>
Click [Generate New Key], select passphrase (32 random, alphanumeric characters are sufficient) and click [OK].

PowerShell

$EnvironmentName = '<ENVIRONMENTPREFIX>'
$ApplicationName = 'Secure Store Service Application'
$ApplicationPoolName = $ApplicationProxyName
$ApplicationPoolAccount = '<APPPOOLACCT (domain\account)>'
$ApplicationProxyName = $ApplicationName
$Auditing = $false

$DBServer = (Get-SPServer | Where-Object {$_.Role -eq 'Invalid'}).Address
$DBName = $EnvironmentName + '_SharePoint_service_'
$ApplicationName.Split(' ') | ForEach-Object {$DBName += $_}

$ManagedAccount = $ApplicationPoolAccount

$ErrorActionPreference = "Stop"
try {Get-SPManagedAccount $ApplicationPoolAccount} catch {New-SPManagedAccount (Get-Credential $ManagedAccount)}
$ErrorActionPreference = "Continue"

New-SPSecureStoreServiceApplication -ApplicationPool (New-SPServiceApplicationPool -Name $ApplicationPoolName -Account (Get-SPManagedAccount $ApplicationPoolAccount)) -AuditingEnabled:$Auditing -DatabaseServer $DBServer -DatabaseName $DBName -Name $ApplicationName
New-SPSecureStoreServiceApplicationProxy -Name $ApplicationProxyName -ServiceApplication (Get-SPServiceApplication | Where-Object {$_.DisplayName -eq $ApplicationName})