Yes, SSL pinning is a possibility. Although as of iOS 10.3, you must take an additional step to trust the Charles Root Certificate that is not currently documented on their website edit: this info is now under iOS Devices here: https://www.charlesproxy.com/documentation/using-charles/ssl-certificates/
Settings > General > About > Certificate Trust Testings
Source: https://www.neglectedpotential.com/2017/04/trusting-custom-root-certificates-on-ios-10-3/