I asked and answered a similar question here. In summary, I add the header once and use it to find the required height. That height can then be applied to the header, and the header is set a second time to reflect the change.

- (void)viewDidLoad
{
    [super viewDidLoad];

    self.header = [[SCAMessageView alloc] init];
    self.header.titleLabel.text = @"Warning";
    self.header.subtitleLabel.text = @"This is a message with enough text to span multiple lines. This text is set at runtime and might be short or long.";

    //set the tableHeaderView so that the required height can be determined
    self.tableView.tableHeaderView = self.header;
    [self.header setNeedsLayout];
    [self.header layoutIfNeeded];
    CGFloat height = [self.header systemLayoutSizeFittingSize:UILayoutFittingCompressedSize].height;

    //update the header's frame and set it again
    CGRect headerFrame = self.header.frame;
    headerFrame.size.height = height;
    self.header.frame = headerFrame;
    self.tableView.tableHeaderView = self.header;
}

If you have multi-line labels, this also relies on the custom view setting the preferredMaxLayoutWidth of each label:

- (void)layoutSubviews
{
    [super layoutSubviews];

    self.titleLabel.preferredMaxLayoutWidth = CGRectGetWidth(self.titleLabel.frame);
    self.subtitleLabel.preferredMaxLayoutWidth = CGRectGetWidth(self.subtitleLabel.frame);
}

or perhaps more generally:

override func layoutSubviews() {
    super.layoutSubviews()  
    for view in subviews {
        guard let label = view as? UILabel where label.numberOfLines == 0 else { continue }
        label.preferredMaxLayoutWidth = CGRectGetWidth(label.frame)
    }
}

Update January 2015

Unfortunately this still seems necessary. Here is a swift version of the layout process:

tableView.tableHeaderView = header
header.setNeedsLayout()
header.layoutIfNeeded()
header.frame.size = header.systemLayoutSizeFittingSize(UILayoutFittingCompressedSize)
tableView.tableHeaderView = header

I’ve found it useful to move this into an extension on UITableView:

extension UITableView {
    //set the tableHeaderView so that the required height can be determined, update the header's frame and set it again
    func setAndLayoutTableHeaderView(header: UIView) {
        self.tableHeaderView = header
        self.tableHeaderView?.translatesAutoresizingMaskIntoConstraints = false
        NSLayoutConstraint.activate([
            header.widthAnchor.constraint(equalTo: self.widthAnchor)
        ])
        header.setNeedsLayout()
        header.layoutIfNeeded()
        header.frame.size =  header.systemLayoutSizeFitting(UIView.layoutFittingCompressedSize)
        self.tableHeaderView = header
    }
}

Usage:

let header = SCAMessageView()
header.titleLabel.text = "Warning"
header.subtitleLabel.text = "Warning message here."
tableView.setAndLayoutTableHeaderView(header)